[BioC] question about DEXSeq from a count table, stopped at estimateExonFoldChanges

[Ou, Jianhong]

Dear Alejandro,

Could you help me to figure out this problem? Thank you. When I try to run DEXSeq from a count table, I got errors:
Error: 3310 errors; first error:
  Error in countsThis[as.character(newMf[i, "exon"]), as.character(newMf[i, : subscript out of bounds

For more information, use bplasterror(). To resume calculation, re-call
  the function and set the argument 'BPRESUME' to TRUE or wrap the
  previous call in bpresume().

First traceback:
  16: DEXSeq(dxd2, reducedModel = ~sample + exon + libtype:exon, fitExpToVar = "treatment", 
          BPPARAM = BPPARAM)
  15: estimateExonFoldChanges(object, fitExpToVar = fitExpToVar)
  14: bplapply(testablegenes, geteffects, BPPARAM = BPPARAM)
  13: bplapply(testablegenes, geteffects, BPPARAM = BPPARAM)
  12: mclapply(X = X, FUN = FUN, ..., mc.set.seed = BPPARAM$setSeed, 
          mc.silent = !BPPARAM$verbose, mc.cores = bpworkers(BPPARAM), 
          mc.cleanup = if (BPPARAM$cleanup) BPPARAM$cleanupSignal else FALSE)
  11: lapply(X = X, FUN = FUN, ...)
  10: lapply(X = X, FUN = FUN, ...)
  9: FUN(c("FBgn0000017", "FBgn0000032", "FBgn0000042", "FBgn0000043", 

Here is my code:
library(DEXSeq)
load(url("http://pgfe.umassmed.edu/ou/bioconductor/RNA-seq/ds3.Rdata"))
BPPARAM = MulticoreParam(workers=4)
dxd2 <- DEXSeqDataSet(countData=ecounts, 
                     sampleData=md,
                     design= ~ sample + exon + treatment:exon + libtype:exon,
                     featureID=eid,
                     groupID=gid)

dxr2 <- DEXSeq(dxd2, 
               reducedModel = ~ sample + exon + libtype:exon, 
               fitExpToVar="treatment",
               BPPARAM=BPPARAM)

sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] DEXSeq_1.10.8           BiocParallel_0.6.1      DESeq2_1.4.5           
 [4] RcppArmadillo_0.4.320.0 Rcpp_0.11.2             GenomicRanges_1.16.4   
 [7] GenomeInfoDb_1.0.2      IRanges_1.22.10         Biobase_2.24.0         
[10] BiocGenerics_0.10.0     BiocInstaller_1.14.2    edgeR_3.6.7            
[13] limma_3.20.8           

loaded via a namespace (and not attached):
 [1] annotate_1.42.1      AnnotationDbi_1.26.0 BatchJobs_1.3       
 [4] BBmisc_1.7           biomaRt_2.20.0       Biostrings_2.32.1   
 [7] bitops_1.0-6         brew_1.0-6           checkmate_1.2       
[10] codetools_0.2-8      DBI_0.2-7            digest_0.6.4        
[13] fail_1.2             foreach_1.4.2        genefilter_1.46.1   
[16] geneplotter_1.42.0   grid_3.1.0           htmltools_0.2.4     
[19] hwriter_1.3          iterators_1.0.7      lattice_0.20-29     
[22] locfit_1.5-9.1       RColorBrewer_1.0-5   RCurl_1.95-4.3      
[25] rmarkdown_0.2.53     Rsamtools_1.16.1     RSQLite_0.11.4      
[28] sendmailR_1.1-2      splines_3.1.0        statmod_1.4.20      
[31] stats4_3.1.0         stringr_0.6.2        survival_2.37-7     
[34] tools_3.1.0          XML_3.98-1.1         xtable_1.7-3        
[37] XVector_0.4.0        yaml_2.1.13          zlibbioc_1.10.0  

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu