Re: question about DEXSeq from a count table, stopped at estimateExonFoldChanges

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" <[email protected]> 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-3WprALB+yeL2fBVCVOL8/[email protected]
>>
>>
>

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