[BioC] how to test for genes of interest?

[Glyn Bradley]

Hi Jenny
I may get shot down horribly for saying this on this list, but isn't
there a large school of thought which says don't do FDR at all, just
take the large list of genes out and mine it for biological
significance.
Certainly a large pharma I've a little experienmce of takes that
approach. Stats are just stats afterall. (and I'm sure you're going to
validate the results with some other wet lab technique anyway).


Glyn PhD
Bioinf and systems modelling
mycib.ac.uk

On Thu, Jul 24, 2008 at 4:14 PM, Jenny Drnevich <drnevich at illinois.edu> wrote:
> Hi everyone,
>
> I've always heard that one of the ways "around" the multiple testing problem
> of microarrays is for you to a priori identify a particular list of genes
> you're interested in, and then you only have to do the multiple test
> correction for this smaller list. I've never done this in practice, and I'm
> not sure at what point in the analysis it's proper to pull out just the
> smaller list. Obviously, all the data preprocessing and normalization will
> be done with all the genes, but should I pull out the genes before fitting
> the model, or after fitting the model right before the multiple test
> adjustment? I'm using the eBayes() shrinkage in limma, so which genes are in
> the model will make a big difference in the outcome.
>
> I'm thinking it would be best to keep all the genes in the model, and then
> split them out into two groups (genes of interest and all the rest) and do a
> FDR correction separately for each group. What do you think?
>
> Thanks,
> Jenny
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
>
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