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Question: EdgeR: Problem with selection of highest transcript
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5.9 years ago by
Guest User12k
Guest User12k wrote:
Hello, when I use this (from carcinoma vs normal example), I select only the lowest transcript instead of the higest: > o <- order(rowSums(y$counts)) > y <- y[o,] > d <- duplicated(y$genes$Symbol) > y <- y[!d,] > nrow(y) what is wrong ? I am a novice in informatics. and I do not know how to save my list of genes (for example after the carcinoma vs normaltissue example). many thanks, Best regards, anna -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] edgeR_3.0.0 limma_3.14.1 -- Sent via the guest posting facility at bioconductor.org. ADD COMMENTlink modified 5.9 years ago by Sean Davis21k • written 5.9 years ago by Guest User12k 0 5.9 years ago by Sean Davis21k United States Sean Davis21k wrote: On Wed, Oct 24, 2012 at 7:28 AM, anna [guest] <guest@bioconductor.org>wrote: > > Hello, when I use this (from carcinoma vs normal example), I select only > the lowest transcript instead of the higest: > > o <- order(rowSums(y$counts)) > This orders the rows from lowest to highest. > > y <- y[o,] > > d <- duplicated(y$genes$Symbol) > This returns TRUE for all duplicates except the first (working from top-to-bottom). > > y <- y[!d,] > This effectively chooses the first row in the list for each Symbol. That will always be the lowest. Given what I have told you above, make a change to your code (perhaps the order() function) that will do what you like. As a general rule, be sure to read the help pages (beginning-to-end) for each function you use. You'll learn a lot from that. Sean > > nrow(y) > > what is wrong ? > I am a novice in informatics. > and I do not know how to save my list of genes (for example after the > carcinoma vs normaltissue example). > many thanks, > Best regards, > anna > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C > [5] LC_TIME=French_France.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] edgeR_3.0.0 limma_3.14.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]