Re: [Mged-mage] [Mged-mage2] MAGE-TAB Illumina question

[Tim R. <ra...@eb...>]

Hi Gavin,

I agree with Michael - this is the way I'd code what you've described in 
MAGE-TAB. The only addition I'd suggest is to add a Label column with the 
label names. A single Labeled Extract can have many Labels; this differs 
from tab2mage, where a separate LE is created for each label. You should 
end up with two rows per hybridization. I've checked, and the current 
parser implementation will support this arrangement (although I don't know 
if the accompanying data file parser copes with idat files as yet). As 
mentioned in my previous email, the feature extraction protocol currently 
has to be combined with the scanning protocol; we may want to consider how 
to fix that at the jamboree.

Cheers,

Tim

-- 

On Sun, 18 Mar 2007, Miller, Michael D (Rosetta) wrote:

> 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
>
>> -----Original Message-----
>> From: mge...@li...
>> [mailto:mge...@li...] On Behalf
>> 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
>>
>> Hi Tim,
>>
>> Do you have any example MAGE-TAB files for Illumina Genotyping?
>> Because there is no sample labeling per se, but instead 2 labels are
>> incorporated during an allele specific extension step, after which
>> you get 2 tiffs (one for each channel) and 2 idat files, I was a
>> little unsure how exactly to deal with this in the sdrf file.  Any
>> pointers would be appreciated,
>>
>> Cheers,
>> Gavin
>>
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>
>