DEXSeq subscript out of bonds error
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@vinkopalada-11051
Last seen 7.7 years ago
Germany

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!

dexseq • 895 views
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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

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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

 

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