[BioC] Almost inexisting overlap of diff. expr. genes foundwhen comparing mas5 / rma

Emmanuel Levy emmanuel.levy at gmail.com
Mon Jul 11 19:39:26 CEST 2005

Dear David and BioC community,

I'd like to be able to give ou an answer but unfortunatly I don't have
enough expertise. 

Still I was wondering about something: there has been a paper out
showing that the "no global change in expression" assumption
widely used when normalising is not very accurate
PMID 15837421
They basicaly use spike in data. Altough I agree with James on the
We did this analysis because my colleagues argue against using the
Affymetrix spike-in data to assess a method because you can always
'tune' a method to work best with the spike-in data, without having any
proof that it works well at all with 'real' data.

In this study they spiked more that 1000 genes. I would tend to think that 
with such a high number the problem of 'tuning' James is pointed out before 
would be far less pronounced.

Do you think that thousands of spiked genes will be part of the next generation
of affymetrix arrays?


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