Wayne,
Thank you for your response.
I thought it was a good idea to use the Detection MAS5 algorithm because 
I remove genes not expressed or expressed a little.
Best regards

  Le 29/10/2010 19:25, wxu a écrit :
> Naima,
> 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:
> http://www.ncbi.nlm.nih.gov/pubmed/20846437
>
> Wayne
> -- 
> 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
>> Saisissez du texte, l'adresse d'un site Web ou importez un document à 
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>> Annuler <http://translate.google.fr/?tr=t&hl=fr>
>>
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