[BioC] Error in DESeqDataSetFromHTSeqCount: scan line did not have 2 elements

Wolfgang Huber whuber at embl.de
Wed Aug 6 18:51:36 CEST 2014


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 Bråte <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 Bråte
> 
>   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
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