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

[Ou, Jianhong]

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
>>
>>
>