[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$countFile),design=sampleTable, flattenedfile=NULL)
Error in `rownames<-`(`*tmp*`, value = c("ENSG00000000003:001", "ENSG00000000003:002", :
attempt to set 'rownames' on an object with no dimensions
I then checked:
> dim(lf)
NULL
> dim(dcounts)
NULL
I generated count files by myself instead of using dexseq_count.py. I tried to follow the standard count file format:
-sh-4.1$ 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
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