[BioC] dexseq read.HTSeqCounts error

Rao,Xiayu XRao at mdanderson.org
Tue Apr 15 17:53:37 CEST 2014

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)
> dim(dcounts)

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


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