Hi, On Wed, Aug 6, 2014 at 5:58 AM, Jon Br?te <jon.brate at="" ibv.uio.no=""> wrote: > Hi, > > I'm having trouble creating a DESeq dataset from HTSeq count files. I find it really strange because it works on other similar count files, but for some reason I get this error: > >> HTSeqCountFilesTest = grep("GFF", list.files(directoryTest), value=TRUE) >> regenerationStageTest = c("DxB1", "DxT3") >> regenerationSamplesTest = c("R3DxB1", "R1DxT3") >> sampleTableTest = data.frame(sampleName=regenerationSamplesTest, fileName=HTSeqCountFilesTest, condition=regenerationStageTest) >> ddsTest = DESeqDataSetFromHTSeqCount(sampleTable=sampleTableTest, directory=directoryTest, design= ~ condition) > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > line 19146 did not have 2 elements Can you hop to line 19146 (+/- 1 line) of the file in question (or all such files you are scanning) to manually explore what's going on here? Should be pretty easy to figure out quickly this way. -steve -- Steve Lianoglou Computational Biologist Genentech

Jon, a possible explanation is that one of your files contains a ?funny? character that is interpreted in unintended manner by ?scan? (e.g. as starting a comment, a quote, or a newline). AfaIcs your attachments neither made it through the mail forwarder nor into the archive (https://stat.ethz.ch/pipermail/bioconductor/2014-August/060899.html ). You could try to resend, or team up with a local R person, set options(error=recover) and debug the scan where it fails. Kind regards Wolfgang Il giorno 06 Aug 2014, alle ore 14:58, Jon Br?te <jon.brate at="" ibv.uio.no=""> ha scritto: > Hi, > > I'm having trouble creating a DESeq dataset from HTSeq count files. I find it really strange because it works on other similar count files, but for some reason I get this error: > >> HTSeqCountFilesTest = grep("GFF", list.files(directoryTest), value=TRUE) >> regenerationStageTest = c("DxB1", "DxT3") >> regenerationSamplesTest = c("R3DxB1", "R1DxT3") >> sampleTableTest = data.frame(sampleName=regenerationSamplesTest, fileName=HTSeqCountFilesTest, condition=regenerationStageTest) >> ddsTest = DESeqDataSetFromHTSeqCount(sampleTable=sampleTableTest, directory=directoryTest, design= ~ condition) > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > line 19146 did not have 2 elements > > > I attach the two count files. > > Thank you > > Jon > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DESeq2_1.4.5 RcppArmadillo_0.4.320.0 Rcpp_0.11.2 > [4] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 > [7] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 RColorBrewer_1.0-5 > [5] RSQLite_0.11.4 XML_3.98-1.1 XVector_0.4.0 annotate_1.42.0 > [9] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 > [13] locfit_1.5-9.1 splines_3.1.0 stats4_3.1.0 survival_2.37-7 > [17] tools_3.1.0 xtable_1.7-3 > > > > > > ---------------------------------------------------------------- > Jon Br??te > > Section for Genetics and Evolutionary Biology (EVOGENE) > Department of Biosciences > University of Oslo > P.B. 1066 Blindern > N-0316, Norway > Email: [1]jon.brate at ibv.uio.no > Phone: 922 44 582 > Web: [2]mn.uio.no/ibv/english/people/aca/jonbra/index.html > > References > > 1. mailto:jon.brate at ibv.uio.no > 2. http://mn.uio.no/ibv/english/people/aca/jonbra/index.html > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor