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Old 06-29-2011, 03:26 PM   #1
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Location: United States

Join Date: Jun 2011
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Default edgeR separate offset values/normalizations for each tag


Thanks in advance for helping. I'm trying to use edgeR on some RNA-Seq data I have to test for differential expression. However, I would like to use a separate normalization value for each tag as opposed to the effective library size calculated by edgeR that's used across the entire sample. Essentially, I want to be able to supply "offset" values as used in glm models per tag as opposed to per sample.

Any idea if edgeR has this flexibility or maybe DESeq?

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Old 07-08-2011, 03:59 PM   #2
Gordon Smyth
Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91

edgeR accepts a matrix value for 'offset', of the same dimensions as the counts. This allows you to specify a separate and possibly different normalization value for every tag in each library.

Best wishes

PS. I read and answer questions on the Bioconductor list regularly, but only occasionally on seqanswers.
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deseq, edger, library size

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