[BioC] how to test for genes of interest?

Gordon K Smyth smyth at wehi.EDU.AU
Sun Jul 27 02:56:00 CEST 2008

Hi Jenny,

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


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

Best wishes

> 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
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu

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