[BioC] edgeR: counts or pseudo.counts?
Davide Cittaro
cittaro.davide at hsr.it
Wed Feb 20 10:26:29 CET 2013
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
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