[BioC] question about DEXSeq from a count table, stopped at estimateExonFoldChanges
Ou, Jianhong
Jianhong.Ou at umassmed.edu
Mon Aug 11 15:15:29 CEST 2014
Dear Alejandro,
Thank you for fix this.
Yours Sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 8/11/14 4:45 AM, "Alejandro Reyes" <alejandro.reyes at embl.de> wrote:
>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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