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

[Steve Lianoglou]

Hi,

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

-- 
Steve Lianoglou
Computational Biologist
Genentech