Bio-Affymetrix
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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>
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<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>
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<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...
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<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     :...
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<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...
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<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 ...
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<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 $...
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<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     : ...

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

    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"summary_statistics"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE27"></A><B>unpack_length_string</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE26">prev</A></TD><TD WIDTH="30"><A HREF="#CODE28">next</A></TD></TR>...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>unpack_length_string</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$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="#0000ff"><b>my</b></font> <font color="#1f32ff">$buffer</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">$len</font> = <font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color="#007400">"V"</font>, <font color="#1f32ff">$buffer</font><font color="#0000ff"...
    <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">$len</font><font color="#0000ff"><b>)</b></font>;

    <font color="#0000ff"><b>return</b></font> <font color="#4169e1"><b>unpack</b></font><font color="#0000ff"><b>(</b></font><font color="#007400">"a"</font>.<font color="#1f32ff">$len</font>,<font color="#1f32ff">$buffer</font><font color="#0000ff"...
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE28"></A><B>write_to_file</B></TD><TD><A HREF="#POD23">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE27">prev</A></TD><TD WIDTH="30"><A HREF="#CODE29">next...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>write_to_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> CDF,<font color="#007400">"&gt;"</font>.<font color="#1f32ff">$filename</font> or <font color="#4169e1"><b>die</b></font> <font color="#007400">"Cannot open file for writing"</font>.<font color="#1f32ff">$...

    <font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">write_to_filehandle</font><font color="#0000ff"><b>(</b></font>\*CDF,<font color="#1f32ff">@_</font><font color="#0000ff"><b>)</b></font>;

    <font color="#4169e1"><b>close</b></font> CDF;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE29"></A><B>write_to_filehandle</B></TD><TD><A HREF="#POD24">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE28">prev</A></TD><TD WIDTH="30">next</TD></TR></...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>write_to_filehandle</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$filehandle</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$format</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$version</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$fake</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font>!<font color="#4169e1"><b>defined</b></font> <font color="#1f32ff">$format</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$format</font>=<font color="#007400">"MAS5"</font>;
	<font color="#1f32ff">$version</font>=12;
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$format</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"XDA"</font> &amp;&amp; !<font color="#4169e1"><b>defined</b></font> <fo...
	<font color="#1f32ff">$version</font>=1;
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$format</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"XDA"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff">...
	<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">_write_xda</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$filehandle</font>,<font color="#1f32ff">$version</font>,<font color="#1f32ff">$fake</font><font color="#0000ff"...
    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$format</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"MAS5"</font><font color="#0000...
	<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">_write_mas5</font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$filehandle</font>,<font color="#1f32ff">$version</font>,<font color="#1f32ff">$fake</font><font color="#0000ff...
    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>else</b></font> <font color="#0000ff"><b>{</b></font>
	croak <font color="#007400">"Format must be XDA or MAS5"</font>;
    <font color="#0000ff"><b>}</b></font></pre>}<BR>
<A NAME="General"></A>
<HR><H2>General documentation</H2>
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<TR BGCOLOR="#4492df"><TD><A NAME="_pod_NOTES"><B>NOTES</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre></pre>
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_REFERENCE"><B>REFERENCE</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>Modules were written with the official Affymetrix documentation, which<BR>can be located at <a href="http://www.affymetrix.com/support/developer/AffxFileFormats.ZIP" target="urlWin">http://...
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_COMPATIBILITY"><B>COMPATIBILITY</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>This module can parse the CHP files produced by the Affymetrix software<BR>MAS 5 and GCOS v1.2. It can also process files produced by GCOS v1.0<BR>in theory. However the authors of this mod...
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_KNOWN BUG"><B>KNOWN BUG</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>Change P Value always comes out wrong when using comparison CHP files<BR>from MAS5. If you have a solution for this, please send email to the<BR>addresses below.<BR></pre>
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_COPYRIGHT"><B>COPYRIGHT</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>Copyright (C) 2005 by Nick James, David J Craigon, NASC (arabidopsis.info), The<BR>University of Nottingham<BR><BR>This module is free software. You can copy or redistribute it under the sa...
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_AUTHORS"><B>AUTHORS</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>    <BR>Nick James (nick at arabidopsis.info)<BR><BR>David J Craigon (david at arabidopsis.info)<BR><BR>Nottingham Arabidopsis Stock Centre (<a href="http://arabidopsis.info" target="urlWin...
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