Hi Mike,

Thank you for the respond, sorry I didn't include those information.

I pasted 3 lines from the HTSeq-count output sam file

PLATYPUS_627RLAAXX:4:001:01065:10528    163     chrX    23803314
50      51M     =       23803885        622
GCCATGGCTACTTGTTTCTGTAATACATGCATGTGTGTTTTTTAAAACCTA
T`cccc^YacbL`TTTa\TTbbbYYcL\c`^cYcc_c^`cc]b]Y\ccbY^     AS:i:0  XN:i:0
XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:51 YT:Z:UU NH:i:1  XF:Z:no_feature
PLATYPUS_627RLAAXX:4:001:01065:11031    97      chr12   56552177
50      12M279N28M875N11M       =       56553900        1868
GCAGTCAAGATGTGTGACTTCACCGAAGACCAGACCGCAGAGTTCAAGGAG
cc`\\dd^dT^ccca`Y`]YYa```TccTab\YL_a`YK`]LK\_]U]]UY     AS:i:0  XM:i:0
XO:i:0  XG:i:0  MD:Z:51 NM:i:0  XS:A:+  NH:i:1  XF:Z:MYL6
PLATYPUS_627RLAAXX:4:001:01065:11031    145     chr12   56553900
50      33M94N18M       =       56552177        -1868
GTGCTGAAATCCGGCATGTTCTTGTCGCACTGGGTGAGAAGATGACAGAGG
a_\L`]TaTTbZU[LZTaRYaTYb`YIZSTZ_]UYQS]]\\`T[``TbT^b     AS:i:-6 XM:i:1
XO:i:0  XG:i:0  MD:Z:26A24      NM:i:1  XS:A:+  NH:i:1  XF:Z:MYL6

In the R package,
I have a data frame looks like:
> table
  samplename    filename condition
1      NML-1 NML-1-htout       NML
2      NML-2 NML-2-htout       NML
3      LMP-1 LMP-1-htout       LMP
4      LMP-2 LMP-2-htout       LMP

Then I call the following in R
cds = newCountDataSetFromHTSeqCount(table, directory=".")


Veronica


On Mon, Jan 27, 2014 at 9:39 AM, Michael Love
<michaelisaiahlove@gmail.com>wrote:

> 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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>>
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