Hi, I'm new to using DESeq and managed to get my data into a CountDataSet object okay. I can figure out how to generate normalised counts by myself, but when I try to set the argument to the count accessor function as described in the documentation, it fails and gives the following message: > counts( "EC1_2_countDataSet", normalized=TRUE) Error in counts("EC1_2_countDataSet", normalized = TRUE) : unused argument(s) (normalized = TRUE) If I look at the man page for "counts" it doesn't list any arguments - could it be that I'm using an obsolete version of DESeq? cheers Jane -- Jane Charlesworth PhD Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.33 Swann Building Mayfield Road Edinburgh EH9 3JR Scotland UK. Email: j <robin.allshire@ed.ac.uk>ane.charlesworth@ed.ac.uk Tel: 44-(0)131-650-7116 [[alternative HTML version deleted]]

On 09/30/2011 03:36 PM, Jane Charlesworth wrote: > Hi, > I'm new to using DESeq and managed to get my data into a CountDataSet object > okay. I can figure out how to generate normalised counts by myself, but when > I try to set the argument to the count accessor function as described in the > documentation, it fails and gives the following message: > >> counts( "EC1_2_countDataSet", normalized=TRUE) > Error in counts("EC1_2_countDataSet", normalized = TRUE) : > unused argument(s) (normalized = TRUE) > > If I look at the man page for "counts" it doesn't list any arguments - could > it be that I'm using an obsolete version of DESeq? The 'normalized' option is only available in the devel version of DESeq. In the release version, you need to write: t(t(counts(cds))/sizefactors(cds)) S