Question: GLM common and trended dispersion EdgeR
0
gravatar for Gordon Smyth
5.8 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k 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 at="" gmail.com=""> > To: bioconductor <bioconductor at="" r-project.org="">, Bioconductor mailing > list <bioconductor at="" 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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ADD COMMENTlink modified 5.8 years ago by Reema Singh570 • written 5.8 years ago by Gordon Smyth39k
Answer: GLM common and trended dispersion EdgeR
0
gravatar for Reema Singh
5.8 years ago by
Reema Singh570
Reema Singh570 wrote:
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 >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:21}}
ADD COMMENTlink written 5.8 years ago by Reema Singh570
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