Re: edgeR: Problem with subsetting a DGEList in latest package version
Steve Lianoglou <lianoglou.steve-RuTDbSqP/[email protected]>
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <CAHA9McNeXg40s1CwhNQ=zB6-gUOt6aVcr3iuMMK9hoXX8hzXVQ@mail.gmail.com> |
On Wed, Aug 13, 2014 at 2:58 PM, Steve Lianoglou <lianoglou.steve-RuTDbSqP/[email protected]> wrote: > Hi, > > On Wed, Aug 13, 2014 at 2:37 PM, Katja Hebestreit <katjah-FGKo4X94FMn2fBVCVOL8/[email protected]> wrote: >> Hello edgeR maintainers, >> >> I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I created it from the HTseq output: >> >> >>> files <- list.files("Gene_counts", >> recursive = FALSE, pattern = "counts", >> full.names=TRUE) >> >>> rc <- readDGE(files, labels = labels) >>> dim(rc) >> [1] 23429 40 >> >>> out1 <- which(colnames(rc) == "PGE_old_E") >>> rc <- rc[,-out1] >> Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : >> replacement has 0 rows, data has 39 > > Can please you show us the output of: > > R> lapply(rc, dim) as well as: R> length(out1) -- Steve Lianoglou Computational Biologist Genentech _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor