Hi, I have recently started working with RNAi screening data and have been
getting up to speed on the literature. I have a few questions ,which are not
directly related to Bioconductor (or R) but I figured that members of the
list would probably be able to help out. If there are more appropriate
places to post such questions I'dd appreciate pointers.

My main question is about hit selection. I'm working with assays in which
each gene is targeted by 4 different siRNA's and the plates have no
replicates. My understanding is that in this situation, one cannot really
use statistical tests to select siRNA's. Instead, one employs threshold
approaches (mean, MAD, quartile etc). Is this correct? In such a
thresholding approach, is there any way one can provide some sort of
significance/score to a selection oh hits?

Would it be correct to say that hit selction is simply a first step and one
should use other informaiton (GO enrichment, pathway analysis) to further
winnow an initial selection of hits?

I am also working on a sensititzation screen, where I am trying to identify
genes that are differentially knocked down. This problem seems analogous to
microarray studies and in that vein, I have been considering the 4 signals
(i.e., 4 siRNA's) for each gene, in the two conditions and used a t-test to
determine whether there is a difference in the means.

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?

Thanks,

-- 
Rajarshi Guha

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