[BioC] edgeR-How to obtain a list of normalized expression values
iaingallagher at btopenworld.com
Fri Mar 16 14:01:52 CET 2012
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
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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