[BioC] dexseq read.HTSeqCounts error

[Alejandro Reyes]

Dear Xiayu Rao,

What is the output of:

all( file.exists(as.character(sampleTable$countfiles)) )

?

Maybe one of your files is corrupted? Do they have all the same number 
of lines?

Best regards,
Alejandro


> Hi, Alejandro and others
>
> Thank you for your information on the forum, which is very helpful. I now have a problem in running dexseq. I need your advice to solve the problem. Any input would be very appreciated.
>
>> ecs <- read.HTSeqCounts(countfiles=as.character(sampleTable$countFile),design=sampleTable, flattenedfile=NULL)
> Error in `rownames<-`(`*tmp*`, value = c("ENSG00000000003:001", "ENSG00000000003:002",  :
>    attempt to set 'rownames' on an object with no dimensions
>
> I then checked:
>> dim(lf)
> NULL
>> dim(dcounts)
> NULL
>
> I generated count files by myself instead of using dexseq_count.py. I tried to follow the standard count file format:
> -sh-4.1$ more SRR791043_count.txt
> ENSG00000000003:001     284
> ENSG00000000003:002     179
> ENSG00000000003:003     275
> ENSG00000000003:004     156
> ENSG00000000003:005     177
> ENSG00000000003:006     157
> ENSG00000000003:007     9
> ENSG00000000003:008     45
> ENSG00000000003:009     4
> ENSG00000000003+ENSG00000102362:001     3
> ............
> Intergene1:001       1
> .........
> intergene2097:001       11
> intergene2098:001       99
> intergene2099:001       54
> intergene2100:001       3
> intergene2101:001       3
> intergene2102:001       20
> intergene2103:001       1
> intergene2104:001       2
> intergene2105:001       1
> intergene2106:001       10
> _ambiguous      0
> _empty  0
> _lowaqual       0
> _notaligned     0
>
>
>> sampleTable
>                                                countFile condition
> SRR791052 SRR791052_count.txt     HER2+
> SRR791054 SRR791054_count.txt     HER2+
> SRR791056 SRR791056_count.txt     HER2+
> SRR791057 SRR791057_count.txt     HER2+
> SRR791058 SRR791058_count.txt     HER2+
> SRR791059 SRR791059_count.txt     HER2+
> SRR791061 SRR791061_count.txt     HER2+
> SRR791062 SRR791062_count.txt     HER2+
> SRR791066 SRR791066_count.txt    Benign
> SRR791067 SRR791067_count.txt    Benign
> SRR791068 SRR791068_count.txt    Benign
> SRR791069 SRR791069_count.txt    Benign
> SRR791070 SRR791070_count.txt    Benign
> SRR791071 SRR791071_count.txt    Benign
> SRR791072 SRR791072_count.txt    Benign
> SRR791073 SRR791073_count.txt    Benign
>
> Note: I am using R 3.0.3 and DEXSeq 1.8.0
>
>
> Thanks,
> Xiayu
>