Dear all,
I have a large RNA-seq data set with 63 samples in 12 condition with different number of replicates. I want to run R on the server to make it faster, but I have this error.
Would you please help me. error:
"Error in lf[[1]] : subscript out of bounds
Calls: DEXSeqDataSetFromHTSeq
Execution halted"

I have R version 3.2.0. here is a short example of the codes I am using:
require("methods")
library("DEXSeq")
library(parallel)

countFiles=list.files(inDir, pattern="*dexseq_count.txt", full.names=TRUE)

flattenedFile = list.files(inDir, pattern="Genecode.v19.DEXSeq.exon-introns.gtf",full.names=TRUE)

sampleTable = data.frame(row.names=factor(c("C1675", "C1492", "D0742", "D0743", "C1670", "C1671")),condition=factor(c("CD_SIG_b", "CD_SIG_nb", "CD_TILE_b", "CD_TILE_b", "CD_TILE_nb", "CD_TILE_nb")),replicate=factor(c("1","2","1","2","1","2")), type=factor(c(rep("paired-end",6))),sex=factor(c("w", "w", "m", "m", "w", "w"))).

Many thanks,

Dear Alejandro,

Thanks for your reply. I am sorry for double posting, I will delete the rest of posts.

Here is:

> sampleAnnotation( dxd )
DataFrame with 63 rows and 5 columns
      sample  condition replicate       type      sex
    <factor>   <factor>  <factor>   <factor> <factor>
1      C1675   CD_SIG_b         1 paired-end        w
2      C1492   CD_SIG_b         2 paired-end        w
3      D0742   CD_SIG_b         3 paired-end        w
4      D0743   CD_SIG_b         4 paired-end        m
5      C1670  CD_SIG_nb         1 paired-end        w
...      ...        ...       ...        ...      ...
59     C1650 UC_TILE_nb         2 paired-end        m
60     C1653 UC_TILE_nb         3 paired-end        w
61     C1652 UC_TILE_nb         4 paired-end        m
62     C2484 UC_TILE_nb         5 paired-end        w
63     C1678 UC_TILE_nb         6 paired-end        w

> colData(dxd)
DataFrame with 126 rows and 6 columns
      sample  condition replicate       type      sex     exon
    <factor>   <factor>  <factor>   <factor> <factor> <factor>
1      C1675   CD_SIG_b         1 paired-end        w     this
2      C1492   CD_SIG_b         2 paired-end        w     this
3      D0742   CD_SIG_b         3 paired-end        w     this
4      D0743   CD_SIG_b         4 paired-end        m     this
5      C1670  CD_SIG_nb         1 paired-end        w     this
...      ...        ...       ...        ...      ...      ...
122    C1650 UC_TILE_nb         2 paired-end        m   others
123    C1653 UC_TILE_nb         3 paired-end        w   others
124    C1652 UC_TILE_nb         4 paired-end        m   others
125    C2484 UC_TILE_nb         5 paired-end        w   others
126    C1678 UC_TILE_nb         6 paired-end        w   others
> head( counts(dxd), 5 )
                        [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
ENSG00000000003.10:E001  422  476  485  220  935  201  103  187  100   458
ENSG00000000003.10:E002  124  159  188   91  336   73   44   58   49   135
ENSG00000000003.10:E003   88  119  124   61  238   54   28   36   44    91
ENSG00000000003.10:E004   83   94   97   49  200   45   18   31   42    91
ENSG00000000003.10:E005   86  109   97   48  222   50   18   33   44    91

I also tried the parallelization to make the DEXSeq to run faster without script (last run took me more that 10 days and I just stop it):

> library(BiocParallel)
> BPPARAM = MultiCoreParam(workers=4)
Error: could not find function "MultiCoreParam"

and I have error.

I am thankful if you can help in any of those errors.

Kind Regards,

Rahel

Dear Alejandro,

Many many thanks for your reply. It worked now.

As I am new in DEXSeq and I just get the data set from a colleagues, What do you mean of paralleize by choromosome number? Do I need to add more choromosome info on my input data?

I am so grateful for your help.

Rahel

Dear Alejandro,

Many thanks for explanation and your help. I am going to run it again. I hope it work now. I might come back with new question!

Kind Regards,

Rahel