[BioC] filter on Human Gene U133 Plus 2

cstrato cstrato at aon.at
Fri Oct 29 21:42:08 CEST 2010

Dear Naima,

Usually I prefer to reduce the number of probesets using "median 
absolute deviation" as prefilter (see e.g. ?madFilter). This reduces the 
number of probesets to about 500-3000 (depending on the cutoff). 
Afterwards I use either unitestFilter and fcFilter (see Chapter 5.2 of 
xps.pdf), or I use the package "limma" which most people use (see 
Appendix A.3 how to create an ExpressionSet for use with limma). 
Generally I do not consider MAS5 detection calls to be sufficient for 

I am sure that other people can give you a more detailed answer, but 
using "moderated t-statistics" is generally a good idea.

Best regards

On 10/29/10 4:45 PM, 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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