[BioC] edgeR: counts or pseudo.counts?

[Davide Cittaro]

On Feb 20, 2013, at 9:22 AM, Mark Robinson <mark.robinson at imls.uzh.ch> wrote:

> 
> 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.
> 

Thanks Mark. Anyway, is it ok to use pseudo counts (if I'm able to explain)? 
Another thing, can I contact you privately when I'll try to implement calcNormFactors and estimateCommonDisp (and equalizeLibSize) in another language? 

Best,

d

> 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
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor