[BioC] multiple testing with 54000 genes

[Sachin Mathur]

Jo,

The number of probes significantly influence  multiple testing
corrections results. .Benjamini and Hoshberg is one of the least
stringent tests.

It works in the following way
1. The p-values of the probes after the t-test are ranked
The largest p-value remains as it is, and starts by testing
2. The second largest p-value of the probe * Number of Probes(p) / p-1
<0.05 and 
for 3rd largest p-value it is 3rd largest p-value  *  p / p-2 <0.05

so if a large number of probes are selected for the test, n/n-1, n/n-2
and so on will beome larger. 

So, selecting lesser number of probes will give you a better result

Sachin.



>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 02/17/05
8:39 AM >>>
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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