Bio-Affymetrix

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lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN

=head1 DESCRIPTION

The Affymetrix microarray system produces files in a variety of
formats. If this means nothing to you, these modules are probably not
for you :). This module parses CHP files. 

This module requires a Bio::Affymetrix::CDF object before it can do
anything. This must be supplied to the constructor. See the perldoc
for that to see how to use that module. The module can parse various
types of CHP file transparently. You can find out what type you have
by using the original_version() method.
    
All of the Bio::Affymetrix modules parse a file entirely into
memory. You therefore need enough memory to hold these objects. For
some applications, parsing as a stream may be more appropriate-
hopefully the source to these modules will give enough clues to make
this an easy task. 

You can also use this software to write CHP files (see the
write_to_file and write_to_filehandle methods). 

lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN

=head2 COMPATIBILITY

This module can parse the CHP files produced by the Affymetrix software
MAS 5 and GCOS v1.2. It can also process files produced by GCOS v1.0
in theory. However the authors of this module have never actually
seen an actual GCOS v1.0 file, and so we rely on the specification
supplied by Affymetrix only. If you have GCOS v1.0 files, feedback
as to whether the code actually works is welcome.

Whatever file format you use the module should work transparently.

These modules are focused on GCOS v1.2 CHP files. The MAS5 CHP
files actually contain a lot of extra information that is not
displayed in MAS5 or GCOS. This information is thrown away by the
parser.

This module can only do expression arrays.

Writing CHP files should work no matter what kind of CHP file was
parsed originally. In other words, you can use these modules as a CHP

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

<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>
</TABLE>
<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...
</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>

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

<A NAME="General"></A>
<HR><H2>General documentation</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<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...
</TD></TR>