Dear Prof Gordon,

Thanks for your suggestion.

Have a nice day.

Best regards,
KJ Lim

On 25 January 2013 03:21, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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@gmail.com>
>> To: Bioconductor mailing list <bioconductor@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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