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This queue is for tickets about the Bio-MAGETAB CPAN distribution.

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The Basics
Id: 94398
Status: resolved
Priority: 0/
Queue: Bio-MAGETAB

People
Owner: TFRAYNER [...] cpan.org
Requestors: mkeays [...] ebi.ac.uk
Cc:
AdminCc:

Bug Information
Severity: Important
Broken in:
  • 1.27
  • 1.28
Fixed in: 1.3



CC: fg_cur [...] ebi.ac.uk
Subject: measurement unit overwritten when measurements have same numeric value but different units
Date: Thu, 03 Apr 2014 09:04:02 +0100
To: bug-Bio-MAGETAB [...] rt.cpan.org
From: Maria Keays <mkeays [...] ebi.ac.uk>
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Dear Tim, When using Bio::MAGETAB we have noticed that in the case where two measurements have the same numeric value but different units (e.g. "2 micromolar" and "2 nanomolar"), only one measurement object is created for the numeric value, and the unit assigned to this object has the value of whatever the last unit assigned to that numeric value in the SDRF was. E.g. in a "FactorValue[dose]\tFactorValue[unit]" column pair, if there is a row with "2\tmicromolar" followed by a row with "2\tnanomolar", only one measurement object with value "2" containing a unit object with value "nanomolar" is created. Conversely, if "2\tmicromolar" is second, the unit object has value "micromolar". The problem goes away if we replace "2\tmicromolar" with "2000\tnanomolar", with two measurement objects being created, so there is a work-around in this case. I am not sure a work-around like this would be sensible for all cases though, for example "2 picomolar" vs. "2 molar" or something like that. Please see the attached files for information: * E-MEXP-3577.nanomolar.sdrf.txt : SDRF with "2\tnanomolar" last. * E-MEXP-3577.factorValues.nanomolar.txt : factorValue objects from Data::Dumper using SDRF with "2\tnanomolar" last. * E-MEXP-3577.micromolar.sdrf.txt : SDRF with "2\tmicromolar" last. * E-MEXP-3577.factorValues.micromolar.txt : factorValue objects from Data::Dumper using SDRF with "2\tmicromolar" last. * E-MEXP-3577.fixed.sdrf.txt : SDRF with "2000\tnanomolar" instead of "2\tmicromolar". * E-MEXP-3577.factorValues.fixed.txt : factorValue objects from Data::Dumper using SDRF with "2000\tnanomolar" instead of "2\tmicromolar". * E-MEXP-3577.idf.txt : IDF file required to parse MAGE-TAB (copying relevant SDRF to E-MEXP-3577.sdrf.txt for each test). The code I used to generate the E-MEXP-3577.factorValues.* files is as follows: --------------------- use Bio::MAGETAB::Util::Reader; my $idf_filename = "E-MEXP-3577.idf.txt"; my $reader = Bio::MAGETAB::Util::Reader->new({ idf => $idf_filename, relaxed_parser => 1, ignore_datafiles => 1, }); my $magetab = $reader->parse; use Data::Dumper; foreach my $factorValue ($magetab->get_factorValues) { print Dumper($factorValue); } --------------------- We are using Bio::MAGETAB version 1.27, on Perl 5.8.8, on Linux (Cent OS). Thanks! Maria Keays -- Maria Keays Functional Genomics European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494546

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RT-Send-CC: fg_cur [...] ebi.ac.uk
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Hi Maria, Thanks very much for bringing this to my attention. I can see immediately from the code where the problem is; it'll probably take a day or two to fix as there's some much-needed refactoring to be done in that area. Cheers, Tim
CC: fg_cur [...] ebi.ac.uk
Subject: Re: [rt.cpan.org #94398] measurement unit overwritten when measurements have same numeric value but different units
Date: Thu, 03 Apr 2014 12:35:12 +0100
To: bug-Bio-MAGETAB [...] rt.cpan.org
From: Maria Keays <mkeays [...] ebi.ac.uk>
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Hi Tim, Great, thanks very much for the quick reply! Maria On 03/04/2014 12:12, Tim Rayner via RT wrote: Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=94398 > > > Hi Maria, > > Thanks very much for bringing this to my attention. I can see immediately from the code where the problem is; it'll probably take a day or two to fix as there's some much-needed refactoring to be done in that area. > > Cheers, > > Tim > >
-- Maria Keays Functional Genomics European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494546


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