[BioC] how to test for genes of interest?

[Gordon K Smyth]

Hi Jenny,

We do this all the time.  Simply subset the fit object that you give to 
topTable() or decideTests(), eg.

   topTable(fit[indicesofinterest,])

It is not usually necessary or desirable to subset before the eBayes() 
step, because that is intended to be whole-genome calculation.

Best wishes
Gordon

> Message: 8
> Date: Thu, 24 Jul 2008 10:14:33 -0500
> From: Jenny Drnevich <drnevich at illinois.edu>
> Subject: [BioC] how to test for genes of interest?
> To: bioconductor at stat.math.ethz.ch
>
> 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