[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
> _______________________________________________
> 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
More information about the Bioconductor
mailing list