guess results from the CPAN

Bio-Affymetrix
<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...
</TD></TR></TABLE>
<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...
</TD></TR></TABLE>
<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>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<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>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<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>;

    <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">"cel_file_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">"cel_file_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="CODE3"></A><B>_parse_mas5</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE2">prev</A></TD><TD WIDTH="30"><A HREF="#CODE4">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff00ff"><b>_parse_mas5</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">"MAS5"</font>;

    <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>;
( run in 2.089 seconds using v1.01-cache-2.11-cpan-75ffa21a3d4 )