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Question: question about DEXSeq from a count table, stopped at estimateExonFoldChanges
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gravatar for Ou, Jianhong
3.4 years ago by
Ou, Jianhong1000
United States
Ou, Jianhong1000 wrote:
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
ADD COMMENTlink modified 3.3 years ago by Alejandro Reyes1.5k • written 3.4 years ago by Ou, Jianhong1000
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gravatar for Alejandro Reyes
3.3 years ago by
Alejandro Reyes1.5k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.5k 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 > >
ADD COMMENTlink written 3.3 years ago by Alejandro Reyes1.5k
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 >> >> >
ADD REPLYlink written 3.3 years ago by Ou, Jianhong1000
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