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

[Michael Love]

on the command line you can do:

head -n 19147 name_of_count_file | tail -n 3



On Wed, Aug 6, 2014 at 1:39 PM, Steve Lianoglou
<lianoglou.steve at gene.com> wrote:
> 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
>
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