[BioC] multiple testing with 54000 genes

[Dipl.-Ing. Johannes Rainer]

good hint, i reduce the list of genes to test on those that have a M 
value bigger than 0.7 (or smaller -0.7) in more than 2 comparisons 
(comparing the 6 hour sample with the 0 hours sample of one patient). 
so i end up with about 4000 probe sets...

Quoting "Oosting, J. (PATH)" <J.Oosting at lumc.nl>:

> Hi,
>
> There are a number of ways to reduce the numebr of genes before the 
> actual analysis. Just beware that your filtering method should not 
> rely on any differences between the groups you test in order to 
> prevent depency of values creeping into your data
> - Remove genes that do not fulfill quality checks (ie expression 
> below or over certain level)
> - Genes that have low overall veriance are probably not regulated
> - Only test genes that are relevant to your experimental question 
> (you should not do this if your question is: "Which genes are 
> differentially expressed between the timepoints" also it is silly to 
> have 2 lists, 1 for the general question and 1 for the specific 
> question.)
>
> Regards,
>
> Jan
>
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch
>> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Dipl.-Ing.
>> Johannes Rainer
>> Sent: donderdag 17 februari 2005 15:39
>> To: bioconductor at stat.math.ethz.ch
>> Subject: [BioC] multiple testing with 54000 genes
>>
>>
>> hi,
>>
>> i wanted to ask if someone has experience in multiple testing with a
>> large number of genes.
>>
>> i have in total 24 Affymetrix chips (hgu133plus2), 12 patients, for
>> every patient an 0 hours and 6 hours after treatment sample. i
>> calculated p values using permutation (mt.maxT function with
>> test="pairt") and corrected for multiple testing using the Benjamini
>> Hochberg method. the problem is, that with that large number of tests
>> (54675 genes and therefore 54675 tests) after adjusting the p
>> values no
>> gene shows a "significant" difference.
>>
>> i will now reduce the number of genes to test to get to some results.
>> has anyone experienced similar problems?
>>
>> thanks, jo
>>
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>