Hello, how can I save my list of differentially expressed genes after having my top DE gene visualized with topTags(lrt)? (I followed step by step the example of carcinoma vs matched normal tissue) thanks, 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 loaded via a namespace (and not attached): [1] tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.

tab <- topTags(lrt) write.table(tab, file="mygenelist.txt") For more details, type ?write.table Gordon > Date: Wed, 24 Oct 2012 02:32:48 -0700 (PDT) > From: "anna [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, m.nadira at yahoo.fr > Subject: [BioC] EdgeR: how to save results for list of genes ? > > > Hello, > how can I save my list of differentially expressed genes after having my top DE gene visualized with topTags(lrt)? > > (I followed step by step the example of carcinoma vs matched normal tissue) > > thanks, > 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 > > loaded via a namespace (and not attached): > [1] tools_2.15.1 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Hello, I mean I want to wite the whole list not only the top genes! I read the help, but I still don't do it correctly. what to do after lrt <- glmLRT(fit) to save data ? thanks, anna tab <- topTags(lrt)   write.table(tab, file="mygenelist.txt") For more details, type ?write.table Gordon >Date: Wed, 24 Oct 2012 02:32:48 -0700 (PDT) >From: "anna [guest]" <guest at="" bioconductor.org=""> >To: bioconductor at r-project.org, m.nadira at yahoo.fr >Subject: [BioC] EdgeR: how to save results for list of genes ? >>> Hello, >how can I save my list of differentially expressed genes after having my top DE gene visualized with topTags(lrt)? >> (I followed step by step the example of carcinoma vs matched normal tissue) >> thanks, >anna [[alternative HTML version deleted]]