This would require the same naming structure of the column titles in the input data frame (degDF) to filterDEGs where the FDR column names are expected to end with "_FDR" and the log fold change columns with "_logFC". Perhaps try it out with the example with edgeR and then make sure your DESeq2 results are provided in the same format. Thomas On Tue, Oct 21, 2014 at 03:40:28PM +0000, Ugo Borello [bioc] wrote: > Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> > > User Ugo Borello<https: support.bioconductor.org="" u="" 5753=""/> wrote Answer: systemPipeR with DESeq2<https: support.bioconductor.org="" p="" 62160="" #62164="">: > > Thank you, Thomas, for your reply. > > > > And what about the filterDEGs() function, could I use it with the results obtained with DESeq2 and then take advantage of the systemPipeR workflow for downstream GO analysis? > > > > Ugo > > ________________________________ > > You may reply via email or visit A: systemPipeR with DESeq2