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Old 04-27-2012, 05:20 AM   #1
nnn
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Default edgeR - Run GLM on only one gene

I would like to use edgeR's GLM functionality to determine the influence of several factors on a gene's expression levels. For performance reasons I would like to estimate the dispersion using the entire count table, but then determine the fit just for the gene I am interested in.

Is there any way to do this, i.e. call glmFit() on just one row of the table? I already tried to create a new CDS for just the gene and copy over the dispersion from the full CDS, but that does not seem to work.
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Old 05-07-2012, 01:42 AM   #2
Gordon Smyth
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If 'y' is your full DGEList object, with common or tagwise dispersions already estimated, you can simply use:

fit <- glmFit(y[i,], design)

where 'i' is any subset of genes you want, even a single gene. The dispersions are automatically subsetted for you.

Note that edgeR is a Bioconductor package, so you can get answers quickly by posting them to the Bioconductor mailing list.

Gordon
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