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CHP documentation.
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<HR><H4>Bio::Affymetrix</H4>
<H3>CHP</H3>
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<TABLE BORDER="1" WIDTH="100%"><TR>
<TD><A HREF="#SUMMARY">Summary</A></TD>
<TD><A HREF="#vardefs">Package variables</A></TD>
<TD><A HREF="#SYNOPSIS">Synopsis</A></TD>
<TD><A HREF="#DESCRIPTION">Description</A></TD>
<TD><A HREF="#General">General documentation</A></TD>
<TD><A HREF="#Methods">Methods</A></TD>
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<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR><TD BGCOLOR="#ffae84"><B>Summary</B></TD></TR>
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<TABLE BORDER="0" WIDTH="100%"><TR><TD><pre><B>Bio::Affymetrix::CHP</B>- parse Affymetrix CHP files<BR></pre></TD></TR>
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<A NAME="vardefs"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Package variables</B></TD>
<TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0" WIDTH="100%"><TR><TD COLSPAN="2">No package variables defined.</TD></TR>
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<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD WIDTH="150"><B>Included modules</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><b><font color="#0000ff">Carp</font></b><...
<TR><TD COLSPAN="2"><b><font color="#0000ff">strict</font></b></TD></TR>
<TR><TD COLSPAN="2"><b><font color="#0000ff">warnings</font></b></TD></TR>
</TABLE>
<A NAME="SYNOPSIS"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Synopsis</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><pre>use Bio::Affymetrix::CHP;<BR><BR>use Bio::Affymetrix::CD...
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<A NAME="DESCRIPTION"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Description</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><pre>The Affymetrix microarray system produces files in a ...
<pre>You fill the object filled with data using the<BR>parse_from_filehandle, parse_from_string or parse_from_file<BR>routines. You can get/set various statistics  using methods on the<BR>object. Data is retrieved as a giant hash from<BR>probe_set_re...
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<A NAME="Methods"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Methods</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE>
<TABLE BORDER="1" CELLSPACING="5"><TR><TD><B>CDF</B></TD><TD><A HREF="#POD1">Description</A></TD><TD><A HREF="#CODE1">Code</A></TD></TR>
<TR><TD><B>CEL_file_name</B></TD><TD><A HREF="#POD2">Description</A></TD><TD><A HREF="#CODE2">Code</A></TD></TR>
<TR><TD><B>_parse_mas5</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE3">Code</A></TD></TR>
<TR><TD><B>_parse_xda</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE4">Code</A></TD></TR>
<TR><TD><B>_write_mas5</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE5">Code</A></TD></TR>
<TR><TD><B>_write_xda</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE6">Code</A></TD></TR>
<TR><TD><B>algorithm_name</B></TD><TD><A HREF="#POD3">Description</A></TD><TD><A HREF="#CODE7">Code</A></TD></TR>
<TR><TD><B>algorithm_params</B></TD><TD><A HREF="#POD4">Description</A></TD><TD><A HREF="#CODE8">Code</A></TD></TR>
<TR><TD><B>algorithm_version</B></TD><TD><A HREF="#POD5">Description</A></TD><TD><A HREF="#CODE9">Code</A></TD></TR>
<TR><TD><B>background_zones</B></TD><TD><A HREF="#POD6">Description</A></TD><TD><A HREF="#CODE10">Code</A></TD></TR>
<TR><TD><B>cols</B></TD><TD><A HREF="#POD7">Description</A></TD><TD><A HREF="#CODE11">Code</A></TD></TR>
<TR><TD><B>new</B></TD><TD><A HREF="#POD8">Description</A></TD><TD><A HREF="#CODE12">Code</A></TD></TR>
<TR><TD><B>original_com_progid</B></TD><TD><A HREF="#POD9">Description</A></TD><TD><A HREF="#CODE13">Code</A></TD></TR>
<TR><TD><B>original_file_name</B></TD><TD><A HREF="#POD10">Description</A></TD><TD><A HREF="#CODE14">Code</A></TD></TR>
<TR><TD><B>original_format</B></TD><TD><A HREF="#POD11">Description</A></TD><TD><A HREF="#CODE15">Code</A></TD></TR>
<TR><TD><B>original_number_of_probes</B></TD><TD><A HREF="#POD12">Description</A></TD><TD><A HREF="#CODE16">Code</A></TD></TR>
<TR><TD><B>original_number_qc_units</B></TD><TD><A HREF="#POD13">Description</A></TD><TD><A HREF="#CODE17">Code</A></TD></TR>
<TR><TD><B>original_version</B></TD><TD><A HREF="#POD14">Description</A></TD><TD><A HREF="#CODE18">Code</A></TD></TR>
<TR><TD><B>parse_from_file</B></TD><TD><A HREF="#POD15">Description</A></TD><TD><A HREF="#CODE19">Code</A></TD></TR>
<TR><TD><B>parse_from_filehandle</B></TD><TD><A HREF="#POD16">Description</A></TD><TD><A HREF="#CODE20">Code</A></TD></TR>
<TR><TD><B>parse_from_string</B></TD><TD><A HREF="#POD17">Description</A></TD><TD><A HREF="#CODE21">Code</A></TD></TR>
<TR><TD><B>probe_array_type</B></TD><TD><A HREF="#POD18">Description</A></TD><TD><A HREF="#CODE22">Code</A></TD></TR>
<TR><TD><B>probe_set_results</B></TD><TD><A HREF="#POD19">Description</A></TD><TD><A HREF="#CODE23">Code</A></TD></TR>
<TR><TD><B>rows</B></TD><TD><A HREF="#POD20">Description</A></TD><TD><A HREF="#CODE24">Code</A></TD></TR>
<TR><TD><B>smooth_factor</B></TD><TD><A HREF="#POD21">Description</A></TD><TD><A HREF="#CODE25">Code</A></TD></TR>
<TR><TD><B>summary_statistics</B></TD><TD><A HREF="#POD22">Description</A></TD><TD><A HREF="#CODE26">Code</A></TD></TR>
<TR><TD><B>unpack_length_string</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE27">Code</A></TD></TR>
<TR><TD><B>write_to_file</B></TD><TD><A HREF="#POD23">Description</A></TD><TD><A HREF="#CODE28">Code</A></TD></TR>
<TR><TD><B>write_to_filehandle</B></TD><TD><A HREF="#POD24">Description</A></TD><TD><A HREF="#CODE29">Code</A></TD></TR>
</TABLE>
<A NAME="MethDesc"></A>
<HR><H2>Methods description</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_CDF"></A><A NAME="POD1"></A><B>CDF</B></TD><TD><A HREF="#CODE1">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD>prev</TD><TD><A HREF="#POD2">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : Bio::Affymetrix::CDF $db_file<BR>  Example    : none<BR>  Description: get/set for CDF file associated with this CHP file. The db is the one that <BR>               belongs to the external_name.  <BR>  Returntype : Bio::Affymetrix...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_CEL_file_name"></A><A NAME="POD2"></A><B>CEL_file_name</B></TD><TD><A HREF="#CODE2">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD1">prev</A></TD><TD><A HREF="#POD3">next</A></TD></TR...
<pre>  Arg [1]    : 	string $cel_file_name (optional)<BR>  Example    : 	my $cel_file_name=$chp-&gt;CEL_file_name();<BR>  Description:	Get/set the CEL file this CHP file was made from<BR>  Returntype :	string<BR>  Exceptions : 	none<BR>  Caller     :...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_algorithm_name"></A><A NAME="POD3"></A><B>algorithm_name</B></TD><TD><A HREF="#CODE7">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD2">prev</A></TD><TD><A HREF="#POD4">next</A></TD></...
<pre>  Arg [1]    : 	string $algorithm_name (optional)<BR>  Example    : 	my $algorithm_name=$chp-&gt;algorithm_name();<BR>  Description:	Get/set the algorithm name that turned the CEL file<BR>into this CHP file<BR>  Returntype :	string<BR>  Exceptio...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_algorithm_params"></A><A NAME="POD4"></A><B>algorithm_params</B></TD><TD><A HREF="#CODE8">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD3">prev</A></TD><TD><A HREF="#POD5">next</A></T...
<pre>  Arg [1]    : 	hashref $algorithm_params (optional)<BR>  Example    : 	my %algorithm_params=%{$chp-&gt;algorithm_params()};<BR><BR># Print scale factor<BR><BR>print $algorithm_params(&quot;SF&quot;);<BR><BR>  Description:	Get/set the algorithm ...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_algorithm_version"></A><A NAME="POD5"></A><B>algorithm_version</B></TD><TD><A HREF="#CODE9">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD4">prev</A></TD><TD><A HREF="#POD6">next</A><...
<pre>  Arg [1]    : 	string $algorithm_version (optional)<BR>  Example    : 	my $algorithm_version=$chp-&gt;algorithm_version();<BR>  Description:	Get/set the algorithm version that turned the CEL file<BR>into this CHP file<BR>  Returntype :	string<B...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_background_zones"></A><A NAME="POD6"></A><B>background_zones</B></TD><TD><A HREF="#CODE10">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD5">prev</A></TD><TD><A HREF="#POD7">next</A></...
<pre>  Arg [1]    : 	arrayref of arrayrefs $background_zones (optional)<BR>  Example    : 	my @background_zones=@{$chp-&gt;background_zones()};<BR><BR># Print &quot;X&quot;, &quot;Y&quot;, &quot;Background Value&quot; for background zone 0<BR>print $...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_cols"></A><A NAME="POD7"></A><B>cols</B></TD><TD><A HREF="#CODE11">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD6">prev</A></TD><TD><A HREF="#POD8">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $x=$chp-&gt;cols()<BR>  Description:	Numbers of columns in the array <BR>  Returntype :	integer<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre>
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<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_new"></A><A NAME="POD8"></A><B>new</B></TD><TD><A HREF="#CODE12">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD7">prev</A></TD><TD><A HREF="#POD9">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : Bio::Affymetrix::CDF $db_file<BR>  Example    : my $chp=new <B>Bio::Affymetrix::CHP</B>($cdf);<BR>  Description: constructor for CHP object<BR>  Returntype : new Bio::Affmetrix::CHP object<BR>  Exceptions : none<BR>  Caller     : ...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_com_progid"></A><A NAME="POD9"></A><B>original_com_progid</B></TD><TD><A HREF="#CODE13">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD8">prev</A></TD><TD><A HREF="#POD10">nex...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $com_id=$chp-&gt;original_com_progid()<BR>  Description:	Gets the progid of the original Microsoft COM object that made<BR>				this CHP file<BR>  Returntype :	string<BR>  Exceptions : 	none<BR>  Caller ...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_file_name"></A><A NAME="POD10"></A><B>original_file_name</B></TD><TD><A HREF="#CODE14">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD9">prev</A></TD><TD><A HREF="#POD11">next...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $chp_file_name=$chp-&gt;original_file_name();<BR>  Description:	If this object was created using parse_from_file, the original filename. Otherwise undef.<BR>  Returntype :	string<BR>  Exceptions : 	none...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_format"></A><A NAME="POD11"></A><B>original_format</B></TD><TD><A HREF="#CODE15">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD10">prev</A></TD><TD><A HREF="#POD12">next</A><...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $format=$chp-&gt;original_format()<BR>  Description: 	Returns the format of the CHP file parsed<BR>  			 	(currently) either &quot;XDA&quot; (which is a GCOS v1.2 format,<BR>				also known as version 4)...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_number_of_probes"></A><A NAME="POD12"></A><B>original_number_of_probes</B></TD><TD><A HREF="#CODE16">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD11">prev</A></TD><TD><A HRE...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $original_probes=$chp-&gt;original_number_of_probes()<BR>  Description:	Gets the original number of probes reported in the<BR>				array.<BR><BR>				The CHP files have the number of probes stored in<BR>	...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_number_qc_units"></A><A NAME="POD13"></A><B>original_number_qc_units</B></TD><TD><A HREF="#CODE17">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD12">prev</A></TD><TD><A HREF=...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $original_qc=$chp-&gt;original_number_qc_units()<BR>  Description:	Gets the original number of QC units in the file.<BR>  Returntype :	integer<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_version"></A><A NAME="POD14"></A><B>original_version</B></TD><TD><A HREF="#CODE18">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD13">prev</A></TD><TD><A HREF="#POD15">next</A...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $version=$chp-&gt;original_version()<BR>  Description: 	Returns the version of the CHP file parsed<BR>  		Best used in conjunction with original_format,<BR>		above. For XDA files, the version is always<...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_parse_from_file"></A><A NAME="POD15"></A><B>parse_from_file</B></TD><TD><A HREF="#CODE19">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD14">prev</A></TD><TD><A HREF="#POD16">next</A><...
<pre>  Arg [1]    : 	string<BR>  Example    : 	$chp-&gt;parse_from_file($chp_filename);<BR>  Description:	Parse a CHP file from a file<BR>  Returntype :	none<BR>  Exceptions : 	dies if can\'t open file<BR>  Caller     : 	general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_parse_from_filehandle"></A><A NAME="POD16"></A><B>parse_from_filehandle</B></TD><TD><A HREF="#CODE20">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD15">prev</A></TD><TD><A HREF="#POD1...
<pre>  Arg [1]    : 	reference to filehandle<BR>  Example    : 	$chp-&gt;parse_from_filehandle(\*STDIN);<BR>  Description:	Parse a CHP file from a filehandle<BR>  Returntype :	none<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_parse_from_string"></A><A NAME="POD17"></A><B>parse_from_string</B></TD><TD><A HREF="#CODE21">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD16">prev</A></TD><TD><A HREF="#POD18">next<...
<pre>  Arg [1]    : 	string<BR>  Example    : 	$chp-&gt;parse_from_string($chp_file_in_a_string);<BR>  Description:	Parse a CHP file from a buffer in memory<BR>  Returntype :	none<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_probe_array_type"></A><A NAME="POD18"></A><B>probe_array_type</B></TD><TD><A HREF="#CODE22">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD17">prev</A></TD><TD><A HREF="#POD19">next</A...
<pre>  Arg [1]    : 	string $array_type (optional)<BR>  Example    : 	my $probe_array_type=$chp-&gt;probe_array_type();<BR>  Description:	Get/set the Affymetrix chip type used in the<BR>production of this CHP file. String is same format as CDF file n...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_probe_set_results"></A><A NAME="POD19"></A><B>probe_set_results</B></TD><TD><A HREF="#CODE23">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD18">prev</A></TD><TD><A HREF="#POD20">next<...
<pre>  Arg [1]    : 	hashref of hashrefs $probe_set_results (optional)<BR>  Example    : 	my %results=%{$chp-&gt;probe_set_results()};<BR>e<BR># Print &quot;Signal&quot;, &quot;Detection Call&quot;, &quot;StatPairsUsed&quot; for my favourite probe<BR...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_rows"></A><A NAME="POD20"></A><B>rows</B></TD><TD><A HREF="#CODE24">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD19">prev</A></TD><TD><A HREF="#POD21">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $y=$chp-&gt;rows()<BR>  Description:	Get/set numbers of rows in the array <BR>  Returntype :	integer<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_smooth_factor"></A><A NAME="POD21"></A><B>smooth_factor</B></TD><TD><A HREF="#CODE25">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD20">prev</A></TD><TD><A HREF="#POD22">next</A></TD>...
<pre>  Arg [1]    : 	float $smooth_factor (optional)<BR>  Example    : 	my $smooth_factor=$chp-&gt;smooth_factor();<BR>  Description:	Get/set the smooth factor. Your guess is as good as<BR>mine as to what this actually is, although it is used in calc...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_summary_statistics"></A><A NAME="POD22"></A><B>summary_statistics</B></TD><TD><A HREF="#CODE26">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD21">prev</A></TD><TD><A HREF="#POD23">nex...
<pre>  Arg [1]    : 	hashref $summary_statistics (optional)<BR>  Example    : 	my %summary_statistics=%{$chp-&gt;summary_statistics()};<BR><BR># Print RawQ<BR><BR>print $chp-&gt;summary_statistics()-&gt;{&quot;RawQ&quot;};<BR><BR>  Description:	Get/s...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_write_to_file"></A><A NAME="POD23"></A><B>write_to_file</B></TD><TD><A HREF="#CODE28">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD22">prev</A></TD><TD><A HREF="#POD24">next</A></TD>...
<pre>  Arg [1]    : 	string $filename<BR>  Arg [2]    : 	string $format<BR>  Arg [3]    : 	string $version<BR>  Example    : 	$cdf-&gt;write_to_file($cdf_filename);<BR>  Description:	Writes a CDF file to a file. See write_to_filehandle for descriptio...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_write_to_filehandle"></A><A NAME="POD24"></A><B>write_to_filehandle</B></TD><TD><A HREF="#CODE29">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD23">prev</A></TD><TD><A HREF="#POD25">n...
<pre>  Arg [1]    : 	filehandle $filehandle<BR>  Arg [2]    : 	string $format<BR>  Arg [3]    : 	string $version<BR>  Example    : 	$chp-&gt;write_to_filehandle(\*STDOUT);<BR>  Description:	Writes a CDF file to a filehandle. Takes arguments of<BR>  t...
<A NAME="MethCode"></A>
<HR><H2>Methods code</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE1"></A><B>CDF</B></TD><TD><A HREF="#POD1">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30">prev</TD><TD WIDTH="30"><A HREF="#CODE2">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>CDF</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE2"></A><B>CEL_file_name</B></TD><TD><A HREF="#POD2">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE1">prev</A></TD><TD WIDTH="30"><A HREF="#CODE3">next</A>...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>CEL_file_name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 


    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$buffer</font>; 
    
    <font color="#ff0000">## Get version from file</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></fo...
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>=<font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="#...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>!=12&amp;&amp;<font...
	carp <font color="#007400">"This CHP file has a version number unrecognised by the software parsing them. Results may be suspect."</font>; <font color="#ff0000">## die here, perhaps?</font><BR>    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>==13<font color="#0...
	carp <font color="#007400">"The authors of this module have never seen a genuine GCOS v1.0 CHP file. This program can parse them, but we're only relying on the specification supplied by Affymetrix- we've not tested this at all. Suspect results there...
    <font color="#0000ff"><b>}</b></font>
    <font color="#ff0000">## Trivia section</font><BR>
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_version"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</f...

    
    <font color="#ff0000">## Parse algorithm parameters to maintain compatability with XDA format</font><BR>
    <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%algorithm_params</font>;
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$parse_me</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="#...
	<font color="#0000ff"><b>foreach</b></font> <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>split</b></font> <font color="#006400"><b>/ /</b></font>,<font color="#1...
	    <font color="#0000ff"><b>my</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$name</font>,<font color="#1f32ff">$value</font><font color="#0000ff"><b>)</b></font>=<font color="#4169e1"><b>split</b></font> <font color="#00640...
	    <font color="#1f32ff">$algorithm_params</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$name</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	<font color="#0000ff"><b>}</b></font>

	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_params"</font><font color="#0000ff"><b>}</b></font>=\<font color="#1f32ff">%algorithm_params</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## Summary statistics</font><BR>
    <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%summary_stats</font>;
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$parse_me</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="#...
	<font color="#0000ff"><b>foreach</b></font> <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>split</b></font> <font color="#006400"><b>/ /</b></font>,<font color="#1...
	    <font color="#0000ff"><b>my</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$name</font>,<font color="#1f32ff">$value</font><font color="#0000ff"><b>)</b></font>=<font color="#4169e1"><b>split</b></font> <font color="#00640...
	    <font color="#1f32ff">$summary_stats</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$name</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	<font color="#0000ff"><b>}</b></font>

	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"summary_statistics"</font><font color="#0000ff"><b>}</b></font>=\<font color="#1f32ff">%summary_stats</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 20<font color="#0000ff"><b>)</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$max_probeset_num</font>;
    <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_rows"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$self</font>-&gt;<font color="#0000...
    
    <font color="#ff0000">## THROW AWAY PROBESET NUMBER FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<font colo...

    <font color="#ff0000">## THROW AWAY NUMBER OF PROBE PAIRS FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<fon...

    <font color="#ff0000">## THROW AWAY PROBESETTYPE FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<font color="...
    <font color="#ff0000">## THROW AWAY PROBESET NUMBER FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<font colo...

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 512<font color="#0000ff"><b>)</b></font>;
    <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$self</font>-&gt;<font col...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font> <font col...
	carp <font color="#007400">"The CDF object you have supplied does not have the same name as the CDF file used to make this CHP file. Results may be dubious"</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><fo...

    <font color="#ff0000">## Actual data. This is the bit that would need to be added to, if we did SNP etc. arrays</font><BR>    <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%data</font>;
	
	<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>==12<font color="#0000...
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%results</font>;
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$probesetlist</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>-&gt;<font color...
	    
	    <font color="#0000ff"><b>foreach</b></font> <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>sort</b></font> <font color="#0000ff"><b>{</b></font><font color="#4...

		<font color="#ff0000">## Non-comparison analysis</font><BR>
		<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 44<font color="#0000ff"><b>)</b></font>;
		
		<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">@results</font>=<font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"V7f3V"</font>, <font color="#1f32ff">$buffer</font><font color="#0000...

		<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%h</font>;

		<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>10<font color="#0000ff"><b>]</b></font>==0<font color="#0000ff"><b>)</b></font> <font color="#0000...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionCall"</font><font color="#0000ff"><b>}</b></font>=<font color="#007400">"P"</font>;
		<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>10<font color="#0000ff"><b>]</b></font>==1<font color="#0...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionCall"</font><font color="#0000ff"><b>}</b></font>=<font color="#007400">"M"</font>;
		<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>10<font color="#0000ff"><b>]</b></font>==2<font color="#0...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionCall"</font><font color="#0000ff"><b>}</b></font>=<font color="#007400">"A"</font>;
		<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>10<font color="#0000ff"><b>]</b></font>==3<font color="#0...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionCall"</font><font color="#0000ff"><b>}</b></font>=<font color="#007400">"N"</font>;
		<font color="#0000ff"><b>}</b></font>

		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionPValue"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>7<font color="#0000ff"...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Signal"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>9<font color="#0000ff"><b>]</b>...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPairs"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>0<font color="#0000ff"><b>]<...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPairsUsed"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>1<font color="#0000ff"><...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Probeset"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#1f32f...

		<font color="#ff0000">## Blimey-o-reilly! There's an entire CEL file in here! Let's ditch that.</font><BR>		
		<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPai...
		<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
		
		<font color="#ff0000">## Comparison analysis</font><BR>
		<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>,<font color="#1f32ff">$buffer</font><font color="#0000ff"><b...
		    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"comparison"</font><font color="#0000ff"><b>}</b></font>=1;
		    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 58<font color="#0000ff"><b>)</b></font>;
		    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">@results</font>=<font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"V5c2l9"</font>,<font color="#1f32ff">$buffer</font><font color="#...

		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Change"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>4<font color="#0000ff"><b>]...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"ChangePValue"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>15<font color="#0000f...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"BaselineAbsent"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>5<font color="#0000...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Probeset"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#1...
		<font color="#0000ff"><b>}</b></font>
		
<font color="#ff0000">##		$probesetlist-&gt;[$i] or die &quot;Suspect CDF file! We have more data in the CHP file than expected. Are you using the right CDF file?&quot;;</font><BR>		
		<font color="#1f32ff">$data</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#1f32ff">$i</font><font color="#0000ff"><b>}</b></font>-&gt;<font color="#ff8204...
		
	    <font color="#0000ff"><b>}</b></font>
	<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000...
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%results</font>;
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$probesetlist</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>-&gt;<font color...

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 


		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"DetectionPValue"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>3<font color="#0000ff"...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Signal"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>4<font color="#0000ff"><b>]</b>...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPairs"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>0<font color="#0000ff"><b>]<...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPairsUsed"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>1<font color="#0000ff"><...
		<font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Probeset"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>[</b></font><font color="#1f32f...

		<font color="#ff0000">## Blimey-o-reilly! There's still-enough-of-a-CEL-file in here to be annoying! Nurse! The screens!</font><BR>		
		<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"StatPai...
		<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
		
		<font color="#ff0000">## Comparison analysis</font><BR>
		<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>,<font color="#1f32ff">$buffer</font><font color="#0000ff"><b...
		    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 27<font color="#0000ff"><b>)</b></font>; <font color="#ff0000">##????????</font><BR>		    <fon...

		    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%h</font>;
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Change"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>1<font color="#0000ff"><b>]...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"ChangePValue"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>6<font color="#0000ff...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"SignalLogRatio"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>3<font color="#0000...
		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"BaselineAbsent"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$results</font><font color="#0000ff"><b>[</b></font>2<font color="#0000...

		    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#007400">"Probeset"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>[</b></font><font color="#1...
		<font color="#0000ff"><b>}</b></font>
		
		<font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>[</b></font><font color="#1f32ff">$i</font><font color="#0000ff"><b>]</b></font> or <font color="#4169e1"><b>die</b></font> <font color="#007400">"Suspect CDF file! We have mor...
		
		<font color="#1f32ff">$data</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$probesetlist</font>-&gt;<font color="#0000ff"><b>[</b></font><font color="#1f32ff">$i</font><font color="#0000ff"><b>]</b></font>-&gt;<font color="#ff8204...
		
	    <font color="#0000ff"><b>}</b></font>
	<font color="#0000ff"><b>}</b></font>

	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_set_results"</font><font color="#0000ff"><b>}</b></font>=\<font color="#1f32ff">%data</font>;
    <font color="#0000ff"><b>}</b></font></pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE4"></A><B>_parse_xda</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE3">prev</A></TD><TD WIDTH="30"><A HREF="#CODE5">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff00ff"><b>_parse_xda</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>,<font color="#1f32ff">$fh</font><font color="#0000ff"><b>)</b></font> = <font color="#1f32ff">@_</font>;

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"format"</font><font color="#0000ff"><b>}</b></font>=<font color="#007400">"XDA"</font>;
    
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$buffer</font>; 

    <font color="#ff0000">## First some trivia</font><BR>
    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>= <font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="...
    
    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>!=1<font color="#00...
	carp <font color="#007400">"This CHP file is newer than the software parsing them. Results may be suspect."</font>; <font color="#ff0000">## die here, perhaps?</font><BR>    <font color="#0000ff"><b>}</b></font>

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 12<font color="#0000ff"><b>)</b></font>;
    <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_cols"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$self</font>-&gt;<font color="#0000...

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"chip_type"</font><font color="#0000ff"><b>}</b></font>=<font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color=...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"chip_type"</font><font color="#0000ff"><b>}</b></font>!=0<font color="#...
	croak <font color="#007400">"This software does not process non-expression arrays"</font>;
    <font color="#0000ff"><b>}</b></font>
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><fo...
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cel_file_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font>...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</fo...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_version"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</f...

    <font color="#ff0000">## Algorithm parameters</font><BR>    
    <font color="#0000ff"><b>{</b></font>
	<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$no_algorithm_params</font> = <font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>, <font color="#1f32ff">$buffer</font><font co...

	<font color="#ff0000">## get varying number of parameter names and values and read into hash </font><BR>	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%algorithm_params</font>; 
	<font color="#0000ff"><b>for</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font>=0;<font color="#1f32ff">$i</font>&lt;<font color="#1f32ff">$no_algorithm_params</font>;<font color="#...
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$name</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="#...
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$value</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="...
	    <font color="#1f32ff">$algorithm_params</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$name</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	<font color="#0000ff"><b>}</b></font>

	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_params"</font><font color="#0000ff"><b>}</b></font>=\<font color="#1f32ff">%algorithm_params</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## Summary statistics</font><BR>
    <font color="#0000ff"><b>{</b></font>
	<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$no_stats</font> = <font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>, <font color="#1f32ff">$buffer</font><font color="#0000f...

	<font color="#ff0000">## get varying number of parameter names and values and read into hash </font><BR>	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%h</font>;
	<font color="#0000ff"><b>for</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font>=0;<font color="#1f32ff">$i</font>&lt;<font color="#1f32ff">$no_stats</font>;<font color="#1f32ff">$i<...
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$name</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="#...
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$value</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="...
	    <font color="#1f32ff">$h</font><font color="#0000ff"><b>{</b></font><font color="#1f32ff">$name</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	<font color="#0000ff"><b>}</b></font>

	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"summary_statistics"</font><font color="#0000ff"><b>}</b></font>=\<font color="#1f32ff">%h</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## Background calculation</font><BR>
    <font color="#0000ff"><b>{</b></font>
	<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 8<font color="#0000ff"><b>)</b></font>;
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$m</font>;
	<font color="#0000ff"><b>(</b></font><font color="#1f32ff">$m</font>,<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"smooth_factor"</font><font color="#0000ff"><b>}</b></font><font color="#0000ff"><...
	
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"zones"</font><font color="#0000ff"><b>}</b></font>=<font color="#0000ff"><b>[</b></font><font color="#0000ff"><b>]</b></font>;

	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%zone_info</font>; 
	<font color="#0000ff"><b>for</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font>=0;<font color="#1f32ff">$i</font>&lt;<font color="#1f32ff">$m</font>;<font color="#1f32ff">$i</font>+...
	    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 12<font color="#0000ff"><b>)</b></font>;
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">@zone</font> = <font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="#007400">"f3"</font>, <font color="#1f32ff">$buffer</font><font color="#0000...
	    <font color="#4169e1"><b>push</b></font> @<font color="#0000ff"><b>{</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"zones"</font><font color="#0000ff"><b>}</b></font><font color="#000...
	<font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## Actual data. This is the bit that would need to be added to, if we did SNP etc. arrays</font><BR>
    <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$size</font>;
	<font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 5<font color="#0000ff"><b>)</b></font>;
	<font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"analysis_type"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$size</font><font color="#0000ff...

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE7"></A><B>algorithm_name</B></TD><TD><A HREF="#POD3">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE6">prev</A></TD><TD WIDTH="30"><A HREF="#CODE8">next</A...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>algorithm_name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_name"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE8"></A><B>algorithm_params</B></TD><TD><A HREF="#POD4">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE7">prev</A></TD><TD WIDTH="30"><A HREF="#CODE9">next<...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>algorithm_params</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_params"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_params"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE9"></A><B>algorithm_version</B></TD><TD><A HREF="#POD5">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE8">prev</A></TD><TD WIDTH="30"><A HREF="#CODE10">nex...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>algorithm_version</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_version"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_version"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE10"></A><B>background_zones</B></TD><TD><A HREF="#POD6">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE9">prev</A></TD><TD WIDTH="30"><A HREF="#CODE11">nex...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>background_zones</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"zones"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"zones"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE11"></A><B>cols</B></TD><TD><A HREF="#POD7">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE10">prev</A></TD><TD WIDTH="30"><A HREF="#CODE12">next</A></TD><...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>cols</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff...
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_cols"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_cols"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE12"></A><B>new</B></TD><TD><A HREF="#POD8">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE11">prev</A></TD><TD WIDTH="30"><A HREF="#CODE13">next</A></TD></...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>new</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$proto</font> = <font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$class</font> = <font color="#4169e1"><b>ref</b></font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$proto</font><font color="#0000ff"><b>)</b></font>||<font color="#1f32f...
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>  = <font color="#0000ff"><b>{</b></font><font color="#0000ff"><b>}</b></font>;

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>(</b></font>!<font color="#4169e1"><b>defined</b></font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="...
	croak <font color="#007400">"Need to supply a Bio::Affymetric::CDF file to Bio::Affymetrix::CHP constructor"</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#4169e1"><b>bless</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>, <font color="#1f32ff">$class</font><font color="#0000ff"><b>)</b></font>;          <font color="#ff0000">## reconsecrate</font><BR>...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE13"></A><B>original_com_progid</B></TD><TD><A HREF="#POD9">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE12">prev</A></TD><TD WIDTH="30"><A HREF="#CODE14"...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_com_progid</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE14"></A><B>original_file_name</B></TD><TD><A HREF="#POD10">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE13">prev</A></TD><TD WIDTH="30"><A HREF="#CODE15"...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_file_name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"file_name"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE15"></A><B>original_format</B></TD><TD><A HREF="#POD11">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE14">prev</A></TD><TD WIDTH="30"><A HREF="#CODE16">ne...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_format</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"format"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE16"></A><B>original_number_of_probes</B></TD><TD><A HREF="#POD12">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE15">prev</A></TD><TD WIDTH="30"><A HREF="#...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_number_of_probes</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_units"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE17"></A><B>original_number_qc_units</B></TD><TD><A HREF="#POD13">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE16">prev</A></TD><TD WIDTH="30"><A HREF="#C...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_number_qc_units</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_qc_units"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE18"></A><B>original_version</B></TD><TD><A HREF="#POD14">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE17">prev</A></TD><TD WIDTH="30"><A HREF="#CODE19">n...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_version</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE19"></A><B>parse_from_file</B></TD><TD><A HREF="#POD15">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE18">prev</A></TD><TD WIDTH="30"><A HREF="#CODE20">ne...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>parse_from_file</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$filename</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#4169e1"><b>open</b></font> CHP,<font color="#007400">"&lt;"</font>.<font color="#1f32ff">$filename</font> or croak <font color="#007400">"Cannot open file "</font>.<font color="#1f32ff">$filename</font>;
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"file_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$filename</font>;

    <font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">parse_from_filehandle</font><font color="#0000ff"><b>(</b></font>\*CHP<font color="#0000ff"><b>)</b></font>;

    <font color="#4169e1"><b>close</b></font> CHP;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE20"></A><B>parse_from_filehandle</B></TD><TD><A HREF="#POD16">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE19">prev</A></TD><TD WIDTH="30"><A HREF="#CODE...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>parse_from_filehandle</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$fh</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#4169e1"><b>binmode</b></font> <font color="#1f32ff">$fh</font>;
    
    <font color="#ff0000">## First step- detect whether it's a GCOS or MAS5 file</font><BR>    
    <font color="#ff0000">## A buffer for reading things into</font><BR>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$buffer</font>; 

    <font color="#ff0000">## XDA files have their first feature as a magic number, 65</font><BR>
    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$magic_number</font> = <font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>, <font color="#1f32ff">$buffer</font><font color="...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$magic_number</font>==65<font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">_parse_xda</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font><font color="#0000ff"><b>)</b></font>;
	<font color="#0000ff"><b>return</b></font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## MAS5 files have their first feature as a string</font><BR>
    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 18, 4<font color="#0000ff"><b>)</b></font>;



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