From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2007-03-18 18:32:23
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hi gavin, i'm not that familiar with the genotyping protocols, so this may be off base, but i would think one could use the 'Labeled Extract Name' column in the order where the labeling occurred. the tiffs i would imagine would be in the 'Image' column with perhaps a Comment column to specify which image it was. if i understand right, the idat files are the Feature Extracted data that's been collapsed per bead type from the raw data, so there could be a 'Scan Name' column with two 'Array Data File' columns for the two idat files, again with a Comment column for each to differentiate which was which. tim discussed some issues around the feature extraction protocol in his 3/16 e-mail which might be relevant. but i'm not sure what meaning the tiff files would have since the idat files are per bead type, not per bead? cheers, michael=20 > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf=20 > Of Gavin Sherlock > Sent: Saturday, March 17, 2007 2:37 PM > To: Tim Rayner > Cc: mged-mage2; MGED-mage > Subject: [Mged-mage2] MAGE-TAB Illumina question >=20 > Hi Tim, >=20 > Do you have any example MAGE-TAB files for Illumina Genotyping? =20 > Because there is no sample labeling per se, but instead 2 labels are =20 > incorporated during an allele specific extension step, after which =20 > you get 2 tiffs (one for each channel) and 2 idat files, I was a =20 > little unsure how exactly to deal with this in the sdrf file. Any =20 > pointers would be appreciated, >=20 > Cheers, > Gavin >=20 > -------------------------------------------------------------- > ----------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the=20 > chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge > &CID=3DDEVDEV > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 >=20 >=20 |