edgeR separate offset values/normalizations for each tag

sruddy · 06-29-2011, 04:26 PM

Hi,

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?

Thanks!

Gordon Smyth · 07-08-2011, 04:59 PM

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
Gordon

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

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06-29-2011, 04:26 PM	#1
sruddy Junior Member Location: United States Join Date: Jun 2011 Posts: 1	edgeR separate offset values/normalizations for each tag Hi, 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? Thanks!

07-08-2011, 04:59 PM	#2
Gordon Smyth Member 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 Gordon PS. I read and answer questions on the Bioconductor list regularly, but only occasionally on seqanswers.