[BioC] Error in DESeqDataSetFromHTSeqCount: scan line did not have 2 elements
Jon Bråte
jon.brate at ibv.uio.no
Wed Aug 6 14:58:04 CEST 2014
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
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