[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


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


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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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