error on detecting regions
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Dear Users, I met an error that struggled me really long time to figure out. I tried to use detectDMR.slideWin() function, but no matter how I change the factors assign to sampleType, it still has the error. I have several different conditions in a factor - Stage (PRE, POST- ACUTE, POST-COL and POST-LAT). I would like to compare POST-ACUTE with PRE. Here are script: Mset.postAcute=Mset[,Mset$Stage=='POST-ACUTE'] postAcute <- Mset.postAcute$Stage Mset.pre=Mset[,Mset$Stage=='PRE'] pre <- Mset.pre$Stage ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre)) Error message: Error in rowcoltt(x, fac, tstatOnly, 1L) : length(fac)=42, ncol(x)=80, should be the same. In addition: Warning messages: 1: Please use rownames. We are switching away from eSet-specific methods. 2: Please use colnames. We are switching away from eSet-specific methods. 3: Please use rownames. We are switching away from eSet-specific methods. 4: Please use colnames. We are switching away from eSet-specific methods. -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) 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] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 GenomicFeatures_1.14.5 [5] methyAnalysis_1.4.2 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [9] AnnotationDbi_1.24.0 lumi_2.14.2 BiocInstaller_1.12.1 VariantAnnotation_1.8.13 [13] Rsamtools_1.14.3 Biostrings_2.30.1 GenomicRanges_1.14.4 XVector_0.2.0 [17] IRanges_1.20.7 ggplot2_1.0.0 phyloseq_1.6.1 picante_1.6-2 [21] nlme_3.1-117 ape_3.1-2 ade4_1.6-2 knitr_1.6 [25] vegan_2.0-10 lattice_0.20-29 permute_0.8-3 biom_0.3.12 [29] metagenomeSeq_1.5.47 devtools_1.5 gplots_2.13.0 RColorBrewer_1.0-5 [33] matrixStats_0.10.0 limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.1 base64_1.1 beanplot_1.1 biomaRt_2.18.0 [7] biovizBase_1.10.8 bitops_1.0-6 bumphunter_1.2.0 caTools_1.17 cluster_1.15.2 codetools_0.2-8 [13] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 evaluate_0.5.5 foreach_1.4.2 [19] formatR_0.10 Formula_1.1-1 gdata_2.13.3 genefilter_1.44.0 genoset_1.14.0 gtable_0.1.2 [25] gtools_3.4.1 Gviz_1.6.0 Hmisc_3.14-4 httr_0.3 igraph_0.7.1 illuminaio_0.4.0 [31] iterators_1.0.7 itertools_0.1-3 KernSmooth_2.23-12 labeling_0.2 latticeExtra_0.6-26 locfit_1.5-9.1 [37] MASS_7.3-33 Matrix_1.1-4 mclust_4.3 memoise_0.2.1 methylumi_2.8.0 mgcv_1.7-29 [43] minfi_1.8.9 multtest_2.18.0 munsell_0.4.2 nleqslv_2.2 nor1mix_1.1-4 pkgmaker_0.22 [49] plyr_1.8.1 preprocessCore_1.24.0 proto_0.3-10 R.methodsS3_1.6.1 Rcpp_0.11.2 RCurl_1.95-4.1 [55] registry_0.2 reshape_0.8.5 reshape2_1.4 RJSONIO_1.2-0.2 rngtools_1.2.4 rtracklayer_1.22.7 [61] scales_0.2.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [67] tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 xtable_1.7-3 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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Pan Du ▴ 440
@pan-du-4636
Last seen 10.2 years ago
Hi Please update your R and methyAnalysis package to the latest released versions (R 3.1.0, methyAnalysis 1.6.0), and send me the error messages and related data if it still happens. Thanks! Pan On Tue, Jun 17, 2014 at 2:30 PM, guest [guest] <guest@bioconductor.org> wrote: > Dear Users, > > I met an error that struggled me really long time to figure out. I tried > to use detectDMR.slideWin() function, but no matter how I change the > factors assign to sampleType, it still has the error. > > I have several different conditions in a factor - Stage (PRE, POST- ACUTE, > POST-COL and POST-LAT). I would like to compare POST-ACUTE with PRE. > > Here are script: > Mset.postAcute=Mset[,Mset$Stage=='POST-ACUTE'] > postAcute <- Mset.postAcute$Stage > Mset.pre=Mset[,Mset$Stage=='PRE'] > pre <- Mset.pre$Stage > > ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre)) > > Error message: > Error in rowcoltt(x, fac, tstatOnly, 1L) : > length(fac)=42, ncol(x)=80, should be the same. > In addition: Warning messages: > 1: Please use rownames. We are switching away from eSet-specific methods. > 2: Please use colnames. We are switching away from eSet-specific methods. > 3: Please use rownames. We are switching away from eSet-specific methods. > 4: Please use colnames. We are switching away from eSet-specific methods. > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.2 (2013-09-25) > 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] grid parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] FDb.InfiniumMethylation.hg19_2.0.10 > BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 > GenomicFeatures_1.14.5 > [5] methyAnalysis_1.4.2 org.Hs.eg.db_2.10.1 > RSQLite_0.11.4 DBI_0.2-7 > [9] AnnotationDbi_1.24.0 lumi_2.14.2 > BiocInstaller_1.12.1 VariantAnnotation_1.8.13 > [13] Rsamtools_1.14.3 Biostrings_2.30.1 > GenomicRanges_1.14.4 XVector_0.2.0 > [17] IRanges_1.20.7 ggplot2_1.0.0 > phyloseq_1.6.1 picante_1.6-2 > [21] nlme_3.1-117 ape_3.1-2 > ade4_1.6-2 knitr_1.6 > [25] vegan_2.0-10 lattice_0.20-29 > permute_0.8-3 biom_0.3.12 > [29] metagenomeSeq_1.5.47 devtools_1.5 > gplots_2.13.0 RColorBrewer_1.0-5 > [33] matrixStats_0.10.0 limma_3.18.13 > Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.1 > base64_1.1 beanplot_1.1 biomaRt_2.18.0 > [7] biovizBase_1.10.8 bitops_1.0-6 bumphunter_1.2.0 > caTools_1.17 cluster_1.15.2 codetools_0.2-8 > [13] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 > doRNG_1.6 evaluate_0.5.5 foreach_1.4.2 > [19] formatR_0.10 Formula_1.1-1 gdata_2.13.3 > genefilter_1.44.0 genoset_1.14.0 gtable_0.1.2 > [25] gtools_3.4.1 Gviz_1.6.0 Hmisc_3.14-4 > httr_0.3 igraph_0.7.1 illuminaio_0.4.0 > [31] iterators_1.0.7 itertools_0.1-3 KernSmooth_2.23-12 > labeling_0.2 latticeExtra_0.6-26 locfit_1.5-9.1 > [37] MASS_7.3-33 Matrix_1.1-4 mclust_4.3 > memoise_0.2.1 methylumi_2.8.0 mgcv_1.7-29 > [43] minfi_1.8.9 multtest_2.18.0 munsell_0.4.2 > nleqslv_2.2 nor1mix_1.1-4 pkgmaker_0.22 > [49] plyr_1.8.1 preprocessCore_1.24.0 proto_0.3-10 > R.methodsS3_1.6.1 Rcpp_0.11.2 RCurl_1.95-4.1 > [55] registry_0.2 reshape_0.8.5 reshape2_1.4 > RJSONIO_1.2-0.2 rngtools_1.2.4 rtracklayer_1.22.7 > [61] scales_0.2.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 stringr_0.6.2 survival_2.37-7 > [67] tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 > xtable_1.7-3 zlibbioc_1.8.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Hi Pan, It still has the error message after the update. There are total 80 samples, but I only picked subgroup 42 samples to compare as mentioned in the first email. > ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre)) Smoothing Chromosome chr1 ... Smoothing Chromosome chr10 ... Smoothing Chromosome chr11 ... Smoothing Chromosome chr12 ... Smoothing Chromosome chr13 ... Smoothing Chromosome chr14 ... Smoothing Chromosome chr15 ... Smoothing Chromosome chr16 ... Smoothing Chromosome chr17 ... Smoothing Chromosome chr18 ... Smoothing Chromosome chr19 ... Smoothing Chromosome chr2 ... Smoothing Chromosome chr20 ... Smoothing Chromosome chr21 ... Smoothing Chromosome chr22 ... Smoothing Chromosome chr3 ... Smoothing Chromosome chr4 ... Smoothing Chromosome chr5 ... Smoothing Chromosome chr6 ... Smoothing Chromosome chr7 ... Smoothing Chromosome chr8 ... Smoothing Chromosome chr9 ... Error in rowcoltt(x, fac, tstatOnly, 1L) : length(fac)=42, ncol(x)=80, should be the same. > 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 grid stats graphics grDevices utils datasets methods base other attached packages: [1] methyAnalysis_1.6.0 methylumi_2.10.0 minfi_1.10.2 bumphunter_1.4.2 [5] locfit_1.5-9.1 iterators_1.0.7 foreach_1.4.2 lattice_0.20-29 [9] matrixStats_0.10.0 ggplot2_1.0.0 reshape2_1.4 scales_0.2.4 [13] FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0 Biostrings_2.32.0 [17] XVector_0.4.0 GenomicFeatures_1.16.2 org.Hs.eg.db_2.14.0 RSQLite_0.11.4 [21] DBI_0.2-7 AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 [25] GenomeInfoDb_1.0.2 IRanges_1.22.9 BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affy_1.42.2 affyio_1.32.0 annotate_1.42.0 base64_1.1 BatchJobs_1.2 BBmisc_1.6 [7] beanplot_1.1 BiocParallel_0.6.1 biomaRt_2.20.0 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 [13] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 [19] fail_1.2 Formula_1.1-1 genefilter_1.46.1 GenomicAlignments_1.0.1 genoset_1.16.2 gtable_0.1.2 [25] Gviz_1.8.3 Hmisc_3.14-4 illuminaio_0.6.0 KernSmooth_2.23-12 latticeExtra_0.6-26 limma_3.20.5 [31] lumi_2.16.0 MASS_7.3-33 Matrix_1.1-4 mclust_4.3 mgcv_1.7-29 multtest_2.20.0 [37] munsell_0.4.2 nleqslv_2.2 nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22 plyr_1.8.1 [43] preprocessCore_1.26.1 proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 [49] registry_0.2 reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.16.1 rtracklayer_1.24.2 sendmailR_1.1-2 [55] siggenes_1.38.0 splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 [61] VariantAnnotation_1.10.2 XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 Thanks From: Pan Du <dupan.mail@gmail.com<mailto:dupan.mail@gmail.com>> Date: Tue, 17 Jun 2014 14:40:38 -0700 To: "Jia, Li (NIH/NCI) [C]" <jial2 at="" mail.nih.gov<mailto:jial2="" at="" mail.nih.gov="">> Cc: "bioconductor at r-project.org<mailto:bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org<mailto:bioconductor="" at="" r-project.org="">> Subject: Re: error on detecting regions Hi Please update your R and methyAnalysis package to the latest released versions (R 3.1.0, methyAnalysis 1.6.0), and send me the error messages and related data if it still happens. Thanks! Pan On Tue, Jun 17, 2014 at 2:30 PM, guest [guest] <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> wrote: Dear Users, I met an error that struggled me really long time to figure out. I tried to use detectDMR.slideWin() function, but no matter how I change the factors assign to sampleType, it still has the error. I have several different conditions in a factor - Stage (PRE, POST- ACUTE, POST-COL and POST-LAT). I would like to compare POST-ACUTE with PRE. Here are script: Mset.postAcute=Mset[,Mset$Stage=='POST-ACUTE'] postAcute <- Mset.postAcute$Stage Mset.pre=Mset[,Mset$Stage=='PRE'] pre <- Mset.pre$Stage ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre)) Error message: Error in rowcoltt(x, fac, tstatOnly, 1L) : length(fac)=42, ncol(x)=80, should be the same. In addition: Warning messages: 1: Please use rownames. We are switching away from eSet-specific methods. 2: Please use colnames. We are switching away from eSet-specific methods. 3: Please use rownames. We are switching away from eSet-specific methods. 4: Please use colnames. We are switching away from eSet-specific methods. -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) 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] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 GenomicFeatures_1.14.5 [5] methyAnalysis_1.4.2 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [9] AnnotationDbi_1.24.0 lumi_2.14.2 BiocInstaller_1.12.1 VariantAnnotation_1.8.13 [13] Rsamtools_1.14.3 Biostrings_2.30.1 GenomicRanges_1.14.4 XVector_0.2.0 [17] IRanges_1.20.7 ggplot2_1.0.0 phyloseq_1.6.1 picante_1.6-2 [21] nlme_3.1-117 ape_3.1-2 ade4_1.6-2 knitr_1.6 [25] vegan_2.0-10 lattice_0.20-29 permute_0.8-3 biom_0.3.12 [29] metagenomeSeq_1.5.47 devtools_1.5 gplots_2.13.0 RColorBrewer_1.0-5 [33] matrixStats_0.10.0 limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.1 base64_1.1 beanplot_1.1 biomaRt_2.18.0 [7] biovizBase_1.10.8 bitops_1.0-6 bumphunter_1.2.0 caTools_1.17 cluster_1.15.2 codetools_0.2-8 [13] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 evaluate_0.5.5 foreach_1.4.2 [19] formatR_0.10 Formula_1.1-1 gdata_2.13.3 genefilter_1.44.0 genoset_1.14.0 gtable_0.1.2 [25] gtools_3.4.1 Gviz_1.6.0 Hmisc_3.14-4 httr_0.3 igraph_0.7.1 illuminaio_0.4.0 [31] iterators_1.0.7 itertools_0.1-3 KernSmooth_2.23-12 labeling_0.2 latticeExtra_0.6-26 locfit_1.5-9.1 [37] MASS_7.3-33 Matrix_1.1-4 mclust_4.3 memoise_0.2.1 methylumi_2.8.0 mgcv_1.7-29 [43] minfi_1.8.9 multtest_2.18.0 munsell_0.4.2 nleqslv_2.2 nor1mix_1.1-4 pkgmaker_0.22 [49] plyr_1.8.1 preprocessCore_1.24.0 proto_0.3-10 R.methodsS3_1.6.1 Rcpp_0.11.2 RCurl_1.95-4.1 [55] registry_0.2 reshape_0.8.5 reshape2_1.4 RJSONIO_1.2-0.2 rngtools_1.2.4 rtracklayer_1.22.7 [61] scales_0.2.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [67] tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 xtable_1.7-3 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">.
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