[BioC] edgeR-How to obtain a list of normalized expression values

Iain Gallagher iaingallagher at btopenworld.com
Fri Mar 16 14:01:52 CET 2012

Hi Philipp

For normalised counts on the log2 scale do:

effective.lib.size <- d$samples$lib.size * d$samples$norm.factors
y <- log2( t(t(d$counts+0.5) / (effective.lib.size+0.5)) )



----- Original Message -----
From: Philipp Brand <Philipp.Brand at uni-duesseldorf.de>
To: bioconductor at r-project.org
Sent: Friday, 16 March 2012, 12:22
Subject: [BioC] edgeR-How to obtain a list of normalized expression values

Hi everybody,

I am relatively new to R, so this might be a stupid question.
I am actually working with edgeR and I'd like to extract a file with the normalized expression values. I do have the normalization factors in the DGEList and the raw values, but I cannot find (or write, it's to early for that because of my scarce knowledge) a function to extract the normalized ones.

Would be nice if somebody could help me with that.

Thanks in advance,

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