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

Steve Lianoglou lianoglou.steve at gene.com
Wed Aug 6 19:39:49 CEST 2014


On Wed, Aug 6, 2014 at 5:58 AM, Jon Bråte <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 Lianoglou
Computational Biologist

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