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Cittaro Davide
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240
@cittaro-davide-5375
Last seen 10.3 years ago
Hello list,
I'm trying to use read counts normalized with edgeR outside R. After a
DGEList has been normalized by TMM and dispersion has been estimate
(at least with estimateCommonDisp) I have at least three ways to
export data:
cpm(y)
cpm(y, normalized.lib.size=T)
y$pseudo.counts
Which would be the most appropriate? Actually I'm having really good
results with pseudo.counts, but I would like to know your opinion
about.
Thanks
d