From dbawils at mac.com  Tue May 17 09:23:18 2005
From: dbawils at mac.com (Susan M. Wilson)
Date: Tue May 17 09:18:19 2005
Subject: [Bioperl-microarray] Problem using ArrayDesign.pm
Message-ID: <578f0a1516e3ae5808ea8c3b099bc22b@mac.com>

Hi,

I admit to being a real beginner, so please excuse.  I am trying to run 
the following code, but receive the error messages shown below it.  The 
errors on line 276 of ArrayDesign.pm repeat as it continues to parse 
the .CEL file.

#!/usr/bin/perl -w
use Bio::Expression::MicroarrayIO;

$stream = Bio::Expression::MicroarrayIO->new(
   '-file' => "AML_139672.CEL",
   '-template' => "HG_U95Av2.CDF",
   '-format' => "affymetrix");

while (my $in = $stream->next_array()) {
   print $in->id."\n";
   }


"my" variable $feature masks earlier declaration in same scope at 
/Library/Perl/5.8.1/Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm 
line 253.
"my" variable $feature masks earlier declaration in same scope at 
/Library/Perl/5.8.1/Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm 
line 299.
Use of uninitialized value in split at 
/Library/Perl/5.8.1/Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm 
line 274, <$t> line 4070.
Use of uninitialized value in string eq at 
/Library/Perl/5.8.1/Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm 
line 276, <$t> line 4070.