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Dear Collegaues,
I´m having a problem with my Dexseq analysis.
I´m at the step when I need to read the data to DEXSeqDataSet object:
dxd = DEXSeqDataSetFromHTSeq(
countFiles,
sampleData=sampleTable,
design= ~ sample + exon + condition:exon,
flattenedfile=flattenedFile )
FlattenedFile and countFiles were both previously defined.
And when I want to run dxd, Im getting the following msg;
Error in FUN(X[[i]], ...) : subscript out of bonds
Does anyone have an idea what´s causing this error and how to solve it?
Many thanks for the advice!
Hi,
Thanks for your interest in DEXSeq. Could you show the first lines of your count files and gtf files? Could you show also your sampleTable and countFiles objects?
Alejandro
As a template for the analysis DEXseq I prepared count files (HTseq) and reference file (GFF) (following the instructions from https://bioconductor.org/packages/devel/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf). Then I started the analysis in DEXseq:
> library(DEXSeq)
> countFiles = list.files("C:\\Desktop\\count files txt", full.name=T)
> countFiles
[1] "C:\\Desktop\\count files txt/my_007-HB828_stranded.txt"
[2] "C:\\\Desktop\\count files txt/my_008-HB518_stranded.txt"
[3] "C:\\Desktop\\count files txt/my_009-HB1040_stranded.txt"
[4] "C:\\Desktop\\count files txt/my_010-HB699_stranded.txt"
[5] "C:\\Desktop\\count files txt/my_011-HB788_stranded.txt"
[6] "C:\\Desktop\\count files txt/my_012-HB789_stranded.txt"
[7] "C:\\Desktop\\count files txt/nomy_001-HB1397_stranded.txt"
[8] "C:\\Desktop\\count files txt/nomy_002-HB868_stranded.txt"
[9] "C:\\Desktop\\count files txt/nomy_003-HB961_stranded.txt"
[10] "C:\\Desktop\\count files txt/nomy_005-HB327_stranded.txt"
[11] "C:\\Desktop\\count files txt/nomy_006-HB641_stranded.txt"
[12] "C:\\Desktop\\count files txt/nomy_013-HB442_stranded.txt"
> flattenedFile = list.files("C:\\Desktop\\HSA.GRCh37.75.gff", full.name=T)
> sampleTable = data.frame(
+ row.names = c ("my_007-HB828_stranded.txt", "my_008-HB518_stranded.txt", "my_009-HB1040_stranded.txt", "my_010-HB699_stranded.txt", "my_011-HB788_stranded.txt", "my_012-HB789_stranded.txt", "nomy_001-HB1397_stranded.txt", "nomy_002-HB868_stranded.txt", "nomy_003-HB961_stranded.txt", "nomy_005-HB327_stranded.txt", "nomy_006-HB641_stranded.txt", "nomy_013-HB442_stranded.txt" ),
+ condition = c ("my", "my", "my", "my", "my", "my", "nomy", "nomy", "nomy", "nomy", "nomy", "nomy" ) )
> sampleTable
condition
my_007-HB828_stranded.txt my
my_008-HB518_stranded.txt my
my_009-HB1040_stranded.txt my
my_010-HB699_stranded.txt my
my_011-HB788_stranded.txt my
my_012-HB789_stranded.txt my
nomy_001-HB1397_stranded.txt nomy
nomy_002-HB868_stranded.txt nomy
nomy_003-HB961_stranded.txt nomy
nomy_005-HB327_stranded.txt nomy
nomy_006-HB641_stranded.txt nomy
nomy_013-HB442_stranded.txt nomy
And then when I have to define object, Im getting the following error msg:
> dxd = DEXSeqDataSetFromHTSeq(
+ countFiles,
+ sampleData=sampleTable,
+ design= ~ sample + exon + condition:exon,
+ flattenedfile=flattenedFile )
Error in FUN(X[[i]], ...) : subscript out of bounds
Do you have an idea what might be a cause of this problem and how to solve it?
Any advice would be much appreciated!
Vinko