[BioC] some questions about RNAi hit selection

[Thomas Hampton]

If you test N genes comparing two conditions, you have run N tests,  
and yeah, adding more conditions
adds more tests, but people tend to ignore that.

There are two questions on the table regarding multiple test correction,
one being "is this effect caused by experimental conditions" and the  
other
being "will people believe my results were caused by experimental  
conditions,
or chalk them up to a random effect"?

The fact that you have spent the money to perform a certain screen  
suggests
that you are not ambivalent about the probability that the null  
hypothesis
may be universally true in your test. You have some prior knowledge that
predisposes you to think otherwise. Also, you do not, from what I  
understand,
have in your hands enough replicate observations to resolve this  
matter using
data from your original screen.

Other people may not view your results the same way, and they may need
independent verification of your effect in some other test, at test  
that would
not suffer from the same sort of multiple hypothesis burden as your  
initial screen.

In my own experience, these independent verifications generally pan  
out, and
the issue of P value correction in the initial screen becomes a moot  
point. I am hoping
an independent test of some sort is not out of the question.

T



On Jul 2, 2009, at 6:13 PM, Rajarshi Guha wrote:

> What I'm a little confused about is to what extent I need to perform
> multiple test corrections on the p-values - does the 'multiple'  
> refer to the
> number of conditions in which the assay is run (drug and no drug) or  
> the
> number of genes being considered?