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 >> >> >