[BioC] filter on Human Gene U133 Plus 2

wxu wxu at msi.umn.edu
Fri Oct 29 19:25:33 CEST 2010

Why do you need to filter genes? For bad quality or some other reasons 
in your mind? Read my recent paper you may have an idea:

Naïma Oumouhou wrote:
> Dear Christian,
> I'm sorry to bother you again : I've got a question about filter on 
> Affymetrix Human gene U133 Plus 2 array.
> I would like to find differentiallty expressed genes between 2 groups of 
> patients (n1=7 and n2=6).
> I have no experience in microarray analyses.
> I read several publications and your xps vignettes but I don't know what 
> I have to do.
> Some people filtered probesets using Detection MAS5 call:probesets that 
> aren't expressed in at least one sample using the  Detection MAS5 
> algorithm are discarded.
> What do you think about this filter?not tight enough?
> After this filter and with my dataset,I still have 26 495 probesets?Is 
> it too much?
> Furthermore, in these remaining probesets, there are affymetrixx control 
> probesets. These probesets have to be removed?At which step?
> After, I use the moderated t-statistics with BH correction. I find no 
> differentiallty expressed genes.
> I wonder if I have to reduce the number of probesets with another filter 
> or with a "Detection filter" tighter?
> Thanks for any help.
> Naïma
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