[BioC] edgeR: counts or pseudo.counts?

[Mark Robinson]

Davide, I recommend:

cpm(y, normalized.lib.size=TRUE)

y$pseudo.counts would or should be quite similar to the CPMs, but the latter is easier to explain.

Best, Mark



On 20.02.2013, at 07:22, Davide Cittaro wrote:

> 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
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