Hi Veronica,

Could you paste the head of the htseq count table file? Maybe there is some
clue as to what is going wrong.

Also it's a good idea to include all your code (command line and R) to help
package maintainers diagnose what might be going on.

Mike
On Jan 26, 2014 6:16 PM, "Xiaoyu Liang" <veronica.xiaoyu@gmail.com> wrote:

> Hi all,
>
> I was trying to use DESeq with the count table obtained from HTSeq-count.
> When I used the function "newCountDataSetFromHTSeqCount", it gave me an
> error complaining some lines of the count table do not have 24 columns.
>
> The error message looks like:
>
> "Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
> na.strings,  :
>   line 5 did not have 24 elements"
>
> I checked the HTSeq-count table results, not only a couple of line don't
> have 24 columns, most of them don't have. So I can't skip those lines.
>
> Is there anything wrong with HTSeq-count results? Would anybody give me any
> suggestions?
>
> Thank you in advance,
> Veronica
>
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