[BioC] illumina --> limma?

[Stefano Calza]

On Fri, Aug 25, 2006 at 09:42:36AM -0400, Sean Davis wrote:
<Sean>Mark, 
<Sean>
<Sean>Have you made any headway with Illumina regarding getting data that is
<Sean>closer to "raw" but still useful?  We are getting the probe-level data
<Sean>dumped from our (which I think is NOT background-subtracted, but correct me
<Sean>if I am wrong), but these data do not conform to the usual Illumina output
<Sean>(different unique ids for the probes), so I really haven't given much
<Sean>thought to using them, particularly since I can't convince our collaborators
<Sean>to make hacks of their scanner config file to get the dumps for all the data
<Sean>we receive.
<Sean>


I guess we are getting something like that, but afaik the dumps are already somehow corrected (and I get some negative values). The scanner itself may do some background correction when dumping numbers. 
You may need to use the raw scanned image, but it may not be possible (if not through an agreement with Illumia).

I'm just trying to understand what's in this data, so correct me if I'm wrong.

Regards,
Stefano

-- 
Stefano Calza, PhD
Researcher - Biostatistician
Sezione di Statistica Medica e Biometria
Dipartimento di Scienze Biomediche e Biotecnologie
Università degli Studi di Brescia - Italy
Viale Europa, 11 25123 Brescia
email: calza at med.unibs.it
Phone: +390303717653
Fax: +390303717488