From bsman at tom.com Sat Mar 6 14:06:16 2004 From: bsman at tom.com (=?gb2312?B?zfXqySwgU2FuIFdhbmc=?=) Date: Sat Mar 6 14:12:01 2004 Subject: [Bioperl-microarray] Strange? Message-ID: <200403061911.i26JBw9Q010379@portal.open-bio.org> Dear bioperl-microarray: I didn't found any analysis function explanation in the document for microarray package ? Best Regards! Yours sincerely ĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦÍġêÉ, San Wang ĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦbsman@tom.com ĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦĦ2004-03-07 ,-,-. ,-,-. ,-,-. ,-,-. ,- / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / `-'-' `-'-' `-'-' `-'-' San Wang Dr. Student Bioinformatics and Gene Network Research Group Zhejiang University P.R.China Address: Room 415# ,Bio-technology Institute, Zhejiang University, Kaixuan Road 268# Hangzhou Zhejiang, P.R.China 310027 Tel: 0086-571-86892051 Fax: 0086-571-86961525 E-mail: bsman@163.com Website: http://www.estarray.org £­£­£­£­£­£­£­£­£­£­ Innovation is everything. When you are on the forefront, you can see what the next innovation needs to be? --- from Robert Noyce, Founder of Intel The more things change, the more they stay the same! The more things seem to be complicated ,the more they are simple in fact! From allenday at ucla.edu Sat Mar 6 15:03:14 2004 From: allenday at ucla.edu (Allen Day) Date: Sat Mar 6 15:08:59 2004 Subject: [Bioperl-microarray] Strange? In-Reply-To: <200403061911.i26JBw9Q010379@portal.open-bio.org> Message-ID: that's because there isn't any right now :) On Sun, 7 Mar 2004, [gb2312] ????, San Wang wrote: > Dear bioperl-microarray: > > I didn't found any analysis function explanation in the document for microarray package ? > > Best Regards! > > Yours sincerely > ????????????????????, San Wang > ????????????????bsman@tom.com > ????????????????????2004-03-07 > ,-,-. ,-,-. ,-,-. ,-,-. ,- > / / \ \ / / \ \ / / \ \ / / \ \ / / > \ \ / / \ \ / / \ \ / / \ \ / / > `-'-' `-'-' `-'-' `-'-' > > > San Wang > Dr. Student > Bioinformatics and Gene Network Research Group > Zhejiang University > P.R.China > > Address: > Room 415# ,Bio-technology Institute, > Zhejiang University, > Kaixuan Road 268# Hangzhou > Zhejiang, P.R.China > 310027 > > Tel: > 0086-571-86892051 > Fax: > 0086-571-86961525 > E-mail: > bsman@163.com > Website: > http://www.estarray.org > > ???????????????????? > Innovation is everything. When you are on the forefront, you can see what the next innovation needs to be? > --- from Robert Noyce, Founder of Intel > The more things change, the more they stay the same! > The more things seem to be complicated ,the more they are simple in fact! > > _______________________________________________ > bioperl-microarray mailing list > bioperl-microarray@bioperl.org > http://portal.open-bio.org/mailman/listinfo/bioperl-microarray > From luwe at mail.nih.gov Wed Mar 3 13:41:04 2004 From: luwe at mail.nih.gov (Lu, Wei (NIH/NCI/NCICB)) Date: Sun May 16 08:25:46 2004 Subject: [Bioperl-microarray] bioperl-microarray install Message-ID: <8A7350C73265A54587D23E30D15D938004174560@nihexchange13.nih.gov> Hi, This is Wei, system engineer, from LPG, NCI/NIH. I am trying to install bio-microarray over the bioperl, but after successfully "make" the module, I got errors on "make test", which showing there is some modules missing as the following. Is there any way I can find these modules? Thanks for your help in advance, Wei Lu PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/affy_u133a_cel............Can't locate Bio/Expression/FeatureSet.pm in @INC (@INC contains: t . /opt/progs/bioperl-microarray/blib/lib /opt/progs/bioperl-microarray/blib/arch /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/5.8.2 /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl) at Bio/Expression/Microarray/Affymetrix/Array.pm line 57. BEGIN failed--compilation aborted at Bio/Expression/Microarray/Affymetrix/Array.pm line 57. Compilation failed in require at t/affy_u133a_cel.t line 32. BEGIN failed--compilation aborted at t/affy_u133a_cel.t line 32. t/affy_u133a_cel............dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-39 Failed 39/39 tests, 0.00% okay t/affy_u133a_stream.........Can't locate Bio/Expression/FeatureSet.pm in @INC (@INC contains: t . /opt/progs/bioperl-microarray/blib/lib /opt/progs/bioperl-microarray/blib/arch /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/5.8.2 /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl) at Bio/Expression/Microarray/Affymetrix/Array.pm line 57. BEGIN failed--compilation aborted at Bio/Expression/Microarray/Affymetrix/Array.pm line 57. Compilation failed in require at t/affy_u133a_stream.t line 32. From mchen at techfak.uni-bielefeld.de Wed Mar 24 13:04:56 2004 From: mchen at techfak.uni-bielefeld.de (Ming Chen) Date: Sun May 16 08:25:47 2004 Subject: [Bioperl-microarray] microarray data IO Message-ID: <40624B20.1050304@techfak.uni-bielefeld.de> Dear Allen, I tried to use the MicroarrayIO module, but failed. could you please help me? it runs on win2k, apache, activeperl, bioperl-1.2.3. the error message is: Bio/Expression/MicroarrayIO/affymetrix.pm: couldn't load affymetrix - for more details on supported formats please see the MicroarrayIO docs. Can't call method "next_array" on an undefined value at microarray.cgi line 12 the code is below: #!c:/perl/bin/perl use Bio::Expression::MicroarrayIO; my $stream = Bio::Expression::MicroarrayIO->new( '-file' => "133a.cel", '-template' => "133a.cdf", '-format' => "affymetrix", ); while ( my $in = $stream->next_array() ) { print $in->id() . "\n"; }