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

Alejandro Reyes alejandro.reyes at embl.de
Mon Aug 11 10:45:10 CEST 2014


Dear Jianhong Ou,

Thanks for reporting this and for your detailed report!  The problem 
seemed to be that you have ":" characters in your exonIDs.

So, you could either remove them before creating the DEXSeqDataSet 
object by doing:

 > eid <- gsub(":", "", eid)

Or you can use the latest development version of DEXSeq (1.11.13), this 
version should handle this characters correctly.

Bests regards,
Alejandro Reyes


Jianhong Ou


> 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
>
>



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