This is one of those quirky R moments, try something like as.integer(as.character(DATA)).
Michael On Mon, Nov 7, 2011 at 4:24 PM, Eric <v_cand...@hotmail.com> wrote: > Hello, > > I have RNAseq data, which I am trying to analyze with DESeq. My file (tab > delimited .txt) appears to be correct: > >>head(myfile) > VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a > ENSG00000253101 0 0 0 0 0 0 > ENSG00000223972 0 0 0 0 0 0... > > However, when I try to analyze the data with > >>cds <- newCountDataSet(myfile,conds) > > I get the following message: > > "Error in newCountDataSet(myfile,conds) : The countData is not integer. > > The problem, as far as I can tell, is that my data are numerical, not > integer, because when I run > >>str(myfile) > 'data.frame': 53433 obs. of 14 variables: > $ VZ_w13 : num 0 0 0 0 8 0 0 0 0 0 ... > > Does anyone have a way to convert my file from numerical to integer? As you > can see, the data are in fact integers are already, so I'm a bit confused. > > Thanks, > Eric > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.