Hi We have a collaborator with RNA-Seq data with no replicates - and yes, I understand the limitations of this. In the egdeR manual, one solution suggested to estimating common dispersion is choosing a value based on experience e.g. "d$common.dispersion <- 0.4". However, this has the disadvantage of not filling up the pseudo.alt slot of the object, which are useful measures of normalised expression. The estimateTagWiseDisp() function then fails. It's fairly trivial to edit the estimateCommonDisp() function to accept a user provided common dispersion value, but I am not sure this is entirely valid. The question being how to populate the pseudo.alt slot when you are estimating the common dispersion parameter yourself, and whether it is even valid to do so. Cheers Mick -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

Hi Mick, > useful measures of normalised expression Would the cpm() function suit your needs? It's not identical to $pseudo.alt, but should be similar. Best, Mark On 25.10.2012, at 17:37, WATSON Mick wrote: > Hi > > We have a collaborator with RNA-Seq data with no replicates - and yes, I understand the limitations of this. > > In the egdeR manual, one solution suggested to estimating common dispersion is choosing a value based on experience e.g. "d$common.dispersion <- 0.4". However, this has the disadvantage of not filling up the pseudo.alt slot of the object, which are useful measures of normalised expression. The estimateTagWiseDisp() function then fails. > > It's fairly trivial to edit the estimateCommonDisp() function to accept a user provided common dispersion value, but I am not sure this is entirely valid. > > The question being how to populate the pseudo.alt slot when you are estimating the common dispersion parameter yourself, and whether it is even valid to do so. > > Cheers > Mick > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin ---------- http://www.fgcz.ch/Bioconductor2012

Dear Mick, When you choose your own value for the dispersion, the intention is that you simply input the pre-determined value into exactTest(), like so: y <- matrix(rnbinom(40,size=1/0.4,mu=10),nrow=20,ncol=2) d <- DGEList(counts=y,group=1:2) et <- exactTest(d,dispersion=0.4) There is no need for the pseudo.counts to be computed. And you can't possibly expect estimateTagwiseDisp() to run, because it needs replicates. If there isn't enough data to estimate a common dispersion, how could there be enough data to estimate tagwise dispersions? If you want to compute the pseudo.counts for another purpose, then the function equalizeLibSizes() is provided: d2 <- equalizeLibSizes(d,dispersion=0.4) But be aware that the edgeR authors have not recommended the pseudo.counts as a measure of normalized expression. Finally, let me mention that the 'pseudo.alt' component has been renamed 'pseudo.counts' in the latest release of edgeR. It is generally advisable to install and work with the current release version of edgeR and Bioconductor. Best wishes Gordon > Date: Thu, 25 Oct 2012 16:37:48 +0100 > From: WATSON Mick <mick.watson at="" roslin.ed.ac.uk=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] Using edgeR with no replicates, estimating dispersion > and the pseudo.alt slot > > Hi > > We have a collaborator with RNA-Seq data with no replicates - and yes, I > understand the limitations of this. > > In the egdeR manual, one solution suggested to estimating common > dispersion is choosing a value based on experience e.g. > "d$common.dispersion <- 0.4". However, this has the disadvantage of not > filling up the pseudo.alt slot of the object, which are useful measures > of normalised expression. The estimateTagWiseDisp() function then > fails. > > It's fairly trivial to edit the estimateCommonDisp() function to accept > a user provided common dispersion value, but I am not sure this is > entirely valid. > > The question being how to populate the pseudo.alt slot when you are > estimating the common dispersion parameter yourself, and whether it is > even valid to do so. > > Cheers > Mick > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}