Dear Prof. Smyth,

First of all, I am really very sorry for late reply.

Sir, We are using both GLMcommon and Trended dispersion before estimating
tagwise dispersion [ As mention in Section 1.4- Quick Start] for our
analysis.  I was just curious about the usage of these function.

Thank you very much for this nice clarification :)

Kind Regards



On Sat, Jan 11, 2014 at 5:56 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Reema,
>
> I am sorry that it is a little confusing.  Let me clarify.
>
> First, we always recommend that you use the full pipeline including
> tagwise dispersions as summarized in Section 1.4 of the User's Guide. This
> is for any RNA-seq experiment with replicates.
>
> Second, the estimateTagwiseDisp() and estimateGLMTagwiseDisp() functions
> always assume a dispersion trend unless you explicitly tell them not to.
> This is so whether or not you have called estimateGLMTrendedDisp() prior to
> estimateGLMTagwiseDisp().
>
> The reason for calling estimateGLMCommonDisp() and
> estimateGLMTrendedDisp() prior to calling estimateGLMTagwiseDisp() is
> partly for diagnostic purposes and partly to give estimateGLMTagwiseDisp()
> a general idea of the magnitude of the dispersions before it estimates the
> tagwise values.  However neither the common or trended dispersions are
> explicitly used in the tagwise estimation scheme; they are used only to
> setup the resolution of the tagwise estimation grid.
>
> The reason that there is no estimateTrendedDisp() step in Section 1.4 is
> just because historically this function didn't exist.  Remember that we
> created the classic estimateTagwiseDisp() pipeline way back in 2006.
> Omitting the trended step makes only a small difference to the final
> tagwise results.
>
> We are gradually revising all the edgeR code to make the classic and glm
> pipelines consistent with one another.  In the latest versions of edgeR,
> you can simply call:
>
>   y <- estimateDisp(y)
>
> or
>
>   y <- estimateDisp(y,design)
>
> and it will do the whole disp estimation pipeline (classic or glm) for you
> at once.
>
> Best wishes
> Gordon
>
>
>  Date: Thu, 9 Jan 2014 14:42:53 +0000
>> From: Reema Singh <reema28sep@gmail.com>
>> To: bioconductor <bioconductor@r-project.org>, Bioconductor mailing
>>         list    <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] GLM common and trended dispersion EdgeR.
>>
>> Dear All,
>>
>> I have a query regarding using estimateGLMCommonDisp and
>> estimateGLMTrendedDisp.
>>
>> It has been mentioned in the EdgeR manual[*Section 2.8.2 :- Estimating
>> Dispersion*] "Note that we need to estimate either common dispersion or
>> trended dispersions prior
>> to the estimation of tagwise dispersions" and "If both exist, the default
>> is to use the trended dispersions". Whereas in case study 4.4[*Section
>> 4.4.4- Estimating the dispersion*] dispersion has been estimated using
>> both
>> common and Trended before computing the tagwise dispersion.
>>
>> Here my queries are:-
>>
>> 1) Is it fine to use both common and trended dispersion?
>> 2) is there any specific conditions to use common or trended dispersion
>> estimation?
>>
>> Kind Regards
>>
>>
>>
>> --
>> Reema Singh
>> Postdoctoral Research Assistant
>> College of Life Sciences
>> University of Dundee,
>> Dundee DD1 4HN, Scotland
>> United Kingdom
>> http://www.compbio.dundee.ac.uk/people.html
>>
>
> ______________________________________________________________________
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