I'm using the "classic" edgeR method and I was wondering if it is okay to add 0.5 to all of my tag counts before I do any processing of the data to make sure edgeR p-values and and logFC are not effected by any genes with 0 counts? If this is okay, do I need to use these column sums as the new lib.size or since it would all be the same for every column would it be unnecessary? I'm referring to doing something like this??? all_counts <- all_counts + 0.5 then preceding with making the DGElist etc. Thanks -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] edgeR_3.4.2 limma_3.18.11 loaded via a namespace (and not attached): [1] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.

On 2/10/2014 12:06 PM, J [guest] wrote: > I'm using the "classic" edgeR method and I was wondering if it is okay to add 0.5 to all of my tag counts before I do any processing of the data to make sure edgeR p-values and and logFC are not effected by any genes with 0 counts? If this is okay, do I need to use these column sums as the new lib.size or since it would all be the same for every column would it be unnecessary? > > I'm referring to doing something like this??? > > all_counts <- all_counts + 0.5 I suppose you could, but you are assuming that the problem of zero counts never occurred to the author of edgeR. Is that really a bet you want to make? And if you want to make that bet, why on earth would you use edgeR? Luckily for all involved, this is a solved problem, and you even get to provide input if you don't like the defaults. See the prior.count argument to ?exactTest. Best, Jim > > then preceding with making the DGElist etc. > > Thanks > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] edgeR_3.4.2 limma_3.18.11 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099