Hi all, I am currently using edgeR within a dog melanoma French project in order to find differentially expressed genes. One of the first steps of edgeR is to normalize the feature count according to the library size of each sample. I am able to find the normalized counts when I use the ‘usual’ approach in the object ‘y$pseudo.counts’ after the dispersion estimation command. But when I use the GLM approach, I can’t find them (neither the information in the documentation nor the counts in any object produced). Where are they stored ? For information, here is the sessionInfo() and maintainers: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_3.2.4 limma_3.16.8 > packageDescription('edgeR')$Maintainer [1] "Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy\n<dmccarthy@wehi.edu.au>, Yunshun Chen <yuchen@wehi.edu.au>,\nGordon Smyth <smyth@wehi.edu.au>" I can’t really choose the software/package versions I am using because I work on a cluster. Cheers, Mathieu Bahin IGDR - Rennes (France) [[alternative HTML version deleted]]

Hi, I believe the pseudo counts are used internally for some of the dispersion estimation methods, but are not indented for other uses. The standard way to get normalized feature abundances from a DGEList is to use the cpm function. -Ryan On Tue Apr 8 08:03:06 2014, Mathieu Bahin wrote: > Hi all, > > I am currently using edgeR within a dog melanoma French project in order to find differentially expressed genes. > > One of the first steps of edgeR is to normalize the feature count according to the library size of each sample. > I am able to find the normalized counts when I use the ?usual? approach in the object ?y$pseudo.counts? after the dispersion estimation command. > But when I use the GLM approach, I can?t find them (neither the information in the documentation nor the counts in any object produced). Where are they stored ? > > For information, here is the sessionInfo() and maintainers: >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_3.2.4 limma_3.16.8 >> packageDescription('edgeR')$Maintainer > [1] "Mark Robinson <mrobinson at="" wehi.edu.au="">, Davis McCarthy\n<dmccarthy at="" wehi.edu.au="">, Yunshun Chen <yuchen at="" wehi.edu.au="">,\nGordon Smyth <smyth at="" wehi.edu.au="">" > > I can?t really choose the software/package versions I am using because I work on a cluster. > > Cheers, > Mathieu Bahin > IGDR - Rennes (France) > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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