[BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp

[Gordon K Smyth]

Dear KJ Lim,

It may depend on the specific data, but I think that

   y <- estimateGLMCommonDisp(y,design)
   y <- estimateGLMTagwiseDisp(y,design,trend=FALSE)

is probably sufficient for SAGE data, whereas

   y <- estimateGLMCommonDisp(y,design)
   y <- estimateGLMTrendedDisp(y,design)
   y <- estimateGLMTagwiseDisp(y,design,trend=TRUE)

is advisable for RNA-seq data.

Best wishes
Gordon


> Date: Wed, 23 Jan 2013 14:01:35 +0200
> From: KJ Lim <jinkeanlim at gmail.com>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp
>
> Dear edgeR community,
>
> Good day.
>
> Please forgive me if I ask a stupid question.
>
> May I ask, using trended dispersion to estimate genewise (tagwise)
> dispersion for multi factors experiment design is better than using common
> dispersion?
>
> Thanks for your time and advice.
>
> Best regards,
> KJ Lim
>

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