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Bio-Affymetrix

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

    }
    return $self->{"summary_statistics"};
}

# Used in calculating background

=head2 smooth_factor

  Arg [1]    : 	float $smooth_factor (optional)
  Example    : 	my $smooth_factor=$chp->smooth_factor();
  Description:	Get/set the smooth factor. Your guess is as good as
mine as to what this actually is, although it is used in calculating
the background. Not available in MAS5 files.
  Returntype :	float
  Exceptions : 	none
  Caller     : 	general

=cut

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

# An arrayref of zones

=head2 background_zones

  Arg [1]    : 	arrayref of arrayrefs $background_zones (optional)
  Example    : 	my @background_zones=@{$chp->background_zones()};

# Print "X", "Y", "Background Value" for background zone 0
print $background_zones[0]->[0],$background_zones[0]->[1],$background_zones[0]->[2];

  Description:	Get/set an array of background zones. Again, your guess is as good as
mine as to what this actually is, although it is used in calculating
the background. Not available in MAS5 files.

Returns an arrayref to an arrayref. Each zone has an array three
values long, which are X,Y and background value respectively.
  Returntype :	arrayref of arrayrefs
  Exceptions : 	none
  Caller     : 	general

=cut

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

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

<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...
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