methyAnalysis error
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@juan-fernandez-tajes-5273
Last seen 10.2 years ago
Dear list I¹m trying to convert a MethyLumi object into a GenoSet object, but when I try the following command I got an error: > methyGenoSet <- MethyLumiM2GenoSet(filt, lib="IlluminaHumanMethylation27k.db") Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", "cg00003994", : attempt to set 'rownames' on an object with no dimensions This is the code I¹m using to generate the MethyLumi object sampledata <- read.table(file="sampledata_2round.txt", header=T, sep="\t") barcodes <- as.character(sampledata$barcodes) mset.raw <- methylumIDAT(barcodes) sampleNames(mset.raw) <- sampledata$Sample_name metadata <- read.table(file="metadata1.txt", header=T, sep="\t", row.names=1) #Removing sample 061268N mset.raw <- mset.raw[, -1] metadata <- metadata[-1, ] pData(mset.raw) <- metadata #Transforming MethyLumi objet in MehyLumiM object mset.lumi <- as(mset.raw, 'MethyLumiM') ##Perform quantile color balance adjustment lumiMethy.c.adj <- lumiMethyC(mset.lumi) ##Perform ssn normalization lumiMethy.c.ssn <- lumiMethyN(lumiMethy.c.adj, method="ssn") ##Filtering sex chromosome probes load("adf.27k.rda") XYs <- subset(adf.27k, Chr=="X" | Chr=="Y") XYs <- as.character(XYs$Illumin_ID) #Filtering just sex chromosome probes XY <- subset(adf.27k, Chr != "X" & Chr != "Y") XYs <- XY$Illumin_ID lumiMethy.c.ssn <- lumiMethy.c.ssn[XYs,] #Filtering probes based on IQR and cutoff = 0.1 filt <- nsFilter(lumiMethy.c.ssn, require.entrez=F, remove.dupEntrez=F, var.func=IQR, var.cutoff=0.1)$eset And my sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_2.0.7 FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 plyr_1.8 pheatmap_0.7.7 [9] genefilter_1.42.0 multtest_2.18.0 annotate_1.38.0 GOstats_2.26.0 [13] graph_1.38.3 Category_2.26.0 IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 [17] lumi_2.14.0 methylumi_2.8.0 matrixStats_0.8.5 ggplot2_0.9.3.1 [21] reshape2_1.2.2 scales_0.2.3 methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 [25] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1 [29] GenomicRanges_1.12.4 IRanges_1.20.2 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 biomaRt_2.16.0 [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 dichromat_2.0-0 [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 gtable_0.1.2 [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 labeling_0.2 [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-29 Matrix_1.0-14 mclust_4.2 mgcv_1.7-26 [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 preprocessCore_1.22.0 [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 reshape_0.8.4 [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 zlibbioc_1.6.0 Thanks Juan ----- Dr. Juan Fernandez-Tajes McCarthy's Group The Wellcome Trust Centre for Human Genetics University of Oxford Jfertaj@well.ox.ac.uk <mailto:jfertaj@well.ox.ac.uk> jfernandezt@udc.es ----- [[alternative HTML version deleted]]
GO convert methylumi genoset GO convert methylumi genoset • 2.4k views
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Pan Du ▴ 440
@pan-du-4636
Last seen 10.2 years ago
"FDb.InfiniumMethylation.hg19" On Fri, Nov 8, 2013 at 2:28 AM, jfertaj <jfernandezt@udc.es> wrote: > Dear list > > I’m trying to convert a MethyLumi object into a GenoSet object, but when I > try the following command I got an error: > > > methyGenoSet <- MethyLumiM2GenoSet(filt, > lib="IlluminaHumanMethylation27k.db") > Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", > "cg00003994", : > attempt to set 'rownames' on an object with no dimensions > > This is the code I’m using to generate the MethyLumi object > > sampledata <- read.table(file="sampledata_2round.txt", header=T, sep="\t") > barcodes <- as.character(sampledata$barcodes) > mset.raw <- methylumIDAT(barcodes) > sampleNames(mset.raw) <- sampledata$Sample_name > metadata <- read.table(file="metadata1.txt", header=T, sep="\t", > row.names=1) > > #Removing sample 061268N > mset.raw <- mset.raw[, -1] > metadata <- metadata[-1, ] > pData(mset.raw) <- metadata > > #Transforming MethyLumi objet in MehyLumiM object > mset.lumi <- as(mset.raw, 'MethyLumiM') > ##Perform quantile color balance adjustment > lumiMethy.c.adj <- lumiMethyC(mset.lumi) > > ##Perform ssn normalization > lumiMethy.c.ssn <- lumiMethyN(lumiMethy.c.adj, method="ssn") > > ##Filtering sex chromosome probes > load("adf.27k.rda") > XYs <- subset(adf.27k, Chr=="X" | Chr=="Y") > XYs <- as.character(XYs$Illumin_ID) > #Filtering just sex chromosome probes > XY <- subset(adf.27k, Chr != "X" & Chr != "Y") > XYs <- XY$Illumin_ID > lumiMethy.c.ssn <- lumiMethy.c.ssn[XYs,] > > #Filtering probes based on IQR and cutoff = 0.1 > filt <- nsFilter(lumiMethy.c.ssn, require.entrez=F, remove.dupEntrez=F, > var.func=IQR, var.cutoff=0.1)$eset > > And my sessionInfo() > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] IlluminaHumanMethylation450k.db_2.0.7 > FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 > BSgenome_1.28.0 > [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 > plyr_1.8 pheatmap_0.7.7 > > [9] genefilter_1.42.0 multtest_2.18.0 > annotate_1.38.0 GOstats_2.26.0 > > [13] graph_1.38.3 Category_2.26.0 > IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 > > [17] lumi_2.14.0 methylumi_2.8.0 > matrixStats_0.8.5 ggplot2_0.9.3.1 > > [21] reshape2_1.2.2 scales_0.2.3 > methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 > > [25] RSQLite_0.11.4 DBI_0.2-7 > AnnotationDbi_1.22.6 Biobase_2.20.1 > > [29] GenomicRanges_1.12.4 IRanges_1.20.2 > BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 > base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 > biomaRt_2.16.0 > [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 > cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 > dichromat_2.0-0 > [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 > genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 > gtable_0.1.2 > [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 > iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 > labeling_0.2 > [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 > MASS_7.3-29 Matrix_1.0-14 mclust_4.2 > mgcv_1.7-26 > [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 > nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 > preprocessCore_1.22.0 > [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 > RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 > reshape_0.8.4 > [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 > rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 > [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 > XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 > zlibbioc_1.6.0 > > Thanks > > Juan > > ----- > Dr. Juan Fernandez-Tajes > McCarthy's Group > The Wellcome Trust Centre for Human Genetics > University of Oxford > Jfertaj@well.ox.ac.uk > jfernandezt@udc.es > ----- > [[alternative HTML version deleted]]
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Pan Du ▴ 440
@pan-du-4636
Last seen 10.2 years ago
Hi Juan I believe the problem was due to the recent update of genoset package. I will further check it. Also can you try using "FDb.InfiniumMethylation.hg19" library instead of " IlluminaHumanMethylation27k.db". "IlluminaHumanMethylation27k.db" and " IlluminaHumanMethylation450k.db" libraries will be deprecated. methyGenoSet <- MethyLumiM2GenoSet(filt, lib="FDb.InfiniumMethylation.hg19" ) Tell me if the problem still exists. Pan On Fri, Nov 8, 2013 at 2:28 AM, jfertaj <jfernandezt@udc.es> wrote: > Dear list > > I’m trying to convert a MethyLumi object into a GenoSet object, but when I > try the following command I got an error: > > > methyGenoSet <- MethyLumiM2GenoSet(filt, > lib="IlluminaHumanMethylation27k.db") > Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", > "cg00003994", : > attempt to set 'rownames' on an object with no dimensions > > This is the code I’m using to generate the MethyLumi object > > sampledata <- read.table(file="sampledata_2round.txt", header=T, sep="\t") > barcodes <- as.character(sampledata$barcodes) > mset.raw <- methylumIDAT(barcodes) > sampleNames(mset.raw) <- sampledata$Sample_name > metadata <- read.table(file="metadata1.txt", header=T, sep="\t", > row.names=1) > > #Removing sample 061268N > mset.raw <- mset.raw[, -1] > metadata <- metadata[-1, ] > pData(mset.raw) <- metadata > > #Transforming MethyLumi objet in MehyLumiM object > mset.lumi <- as(mset.raw, 'MethyLumiM') > ##Perform quantile color balance adjustment > lumiMethy.c.adj <- lumiMethyC(mset.lumi) > > ##Perform ssn normalization > lumiMethy.c.ssn <- lumiMethyN(lumiMethy.c.adj, method="ssn") > > ##Filtering sex chromosome probes > load("adf.27k.rda") > XYs <- subset(adf.27k, Chr=="X" | Chr=="Y") > XYs <- as.character(XYs$Illumin_ID) > #Filtering just sex chromosome probes > XY <- subset(adf.27k, Chr != "X" & Chr != "Y") > XYs <- XY$Illumin_ID > lumiMethy.c.ssn <- lumiMethy.c.ssn[XYs,] > > #Filtering probes based on IQR and cutoff = 0.1 > filt <- nsFilter(lumiMethy.c.ssn, require.entrez=F, remove.dupEntrez=F, > var.func=IQR, var.cutoff=0.1)$eset > > And my sessionInfo() > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] IlluminaHumanMethylation450k.db_2.0.7 > FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 > BSgenome_1.28.0 > [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 > plyr_1.8 pheatmap_0.7.7 > > [9] genefilter_1.42.0 multtest_2.18.0 > annotate_1.38.0 GOstats_2.26.0 > > [13] graph_1.38.3 Category_2.26.0 > IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 > > [17] lumi_2.14.0 methylumi_2.8.0 > matrixStats_0.8.5 ggplot2_0.9.3.1 > > [21] reshape2_1.2.2 scales_0.2.3 > methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 > > [25] RSQLite_0.11.4 DBI_0.2-7 > AnnotationDbi_1.22.6 Biobase_2.20.1 > > [29] GenomicRanges_1.12.4 IRanges_1.20.2 > BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 > base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 > biomaRt_2.16.0 > [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 > cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 > dichromat_2.0-0 > [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 > genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 > gtable_0.1.2 > [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 > iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 > labeling_0.2 > [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 > MASS_7.3-29 Matrix_1.0-14 mclust_4.2 > mgcv_1.7-26 > [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 > nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 > preprocessCore_1.22.0 > [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 > RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 > reshape_0.8.4 > [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 > rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 > [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 > XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 > zlibbioc_1.6.0 > > Thanks > > Juan > > ----- > Dr. Juan Fernandez-Tajes > McCarthy's Group > The Wellcome Trust Centre for Human Genetics > University of Oxford > Jfertaj@well.ox.ac.uk > jfernandezt@udc.es > ----- > [[alternative HTML version deleted]]
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@juan-fernandez-6235
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Dear list I’m trying to convert a MethyLumi object into a GenoSet object, but when I try the following command I got an error: > methyGenoSet <- MethyLumiM2GenoSet(filt, lib="IlluminaHumanMethylation27k.db") Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", "cg00003994", : attempt to set 'rownames' on an object with no dimensions This is the code I’m using to generate the MethyLumi object sampledata <- read.table(file="sampledata_2round.txt", header=T, sep="\t") barcodes <- as.character(sampledata$barcodes) mset.raw <- methylumIDAT(barcodes) sampleNames(mset.raw) <- sampledata$Sample_name metadata <- read.table(file="metadata1.txt", header=T, sep="\t", row.names=1) #Removing sample 061268N mset.raw <- mset.raw[, -1] metadata <- metadata[-1, ] pData(mset.raw) <- metadata #Transforming MethyLumi objet in MehyLumiM object mset.lumi <- as(mset.raw, 'MethyLumiM') ##Perform quantile color balance adjustment lumiMethy.c.adj <- lumiMethyC(mset.lumi) ##Perform ssn normalization lumiMethy.c.ssn <- lumiMethyN(lumiMethy.c.adj, method="ssn") ##Filtering sex chromosome probes load("adf.27k.rda") XYs <- subset(adf.27k, Chr=="X" | Chr=="Y") XYs <- as.character(XYs$Illumin_ID) #Filtering just sex chromosome probes XY <- subset(adf.27k, Chr != "X" & Chr != "Y") XYs <- XY$Illumin_ID lumiMethy.c.ssn <- lumiMethy.c.ssn[XYs,] #Filtering probes based on IQR and cutoff = 0.1 filt <- nsFilter(lumiMethy.c.ssn, require.entrez=F, remove.dupEntrez=F, var.func=IQR, var.cutoff=0.1)$eset And my sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_2.0.7 FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 plyr_1.8 pheatmap_0.7.7 [9] genefilter_1.42.0 multtest_2.18.0 annotate_1.38.0 GOstats_2.26.0 [13] graph_1.38.3 Category_2.26.0 IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 [17] lumi_2.14.0 methylumi_2.8.0 matrixStats_0.8.5 ggplot2_0.9.3.1 [21] reshape2_1.2.2 scales_0.2.3 methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 [25] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1 [29] GenomicRanges_1.12.4 IRanges_1.20.2 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 biomaRt_2.16.0 [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 dichromat_2.0-0 [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 gtable_0.1.2 [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 labeling_0.2 [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-29 Matrix_1.0-14 mclust_4.2 mgcv_1.7-26 [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 preprocessCore_1.22.0 [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 reshape_0.8.4 [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 zlibbioc_1.6.0 Thanks Juan ----- Dr. Juan Fernandez-Tajes McCarthy's Group The Wellcome Trust Centre for Human Genetics University of Oxford Jfertaj@well.ox.ac.uk<mailto:jfertaj@well.ox.ac.uk> ----- [[alternative HTML version deleted]]
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@juan-fernandez-tajes-5273
Last seen 10.2 years ago
Dear list and Pan, I¹m still having some problems with the methyAnalysis package, after update some functions thanks to Pan I¹m still experiencing some problems with certain functions, for example I am not able to plot the heatmap with >heatmapByChromosome(methyGenoSet, gene='55342', genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', includeGeneBody=TRUE) Error in .local(range, ...) : could not find function "restoreSeqlevels" Error: could not find function "restoreSeqlevels" or annotate the DMR regions with >DMRInfo.ann <- annotateDMRInfo(allDMRInfo, 'TxDb.Hsapiens.UCSC.hg19.knownGene') There were 50 or more warnings (use warnings() to see the first 50) Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), what = c("sequence", : sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY have incompatible genomes: - in 'x': , , , , , , , , , , , , , , , , , , , , , , , - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19 Here is my sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_2.0.7 FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0 [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 plyr_1.8 pheatmap_0.7.7 [9] genefilter_1.42.0 multtest_2.18.0 annotate_1.38.0 GOstats_2.26.0 [13] graph_1.38.3 Category_2.26.0 IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 [17] lumi_2.14.0 methylumi_2.8.0 matrixStats_0.8.5 ggplot2_0.9.3.1 [21] reshape2_1.2.2 scales_0.2.3 methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 [25] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1 [29] GenomicRanges_1.12.4 IRanges_1.20.2 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 biomaRt_2.16.0 [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 dichromat_2.0-0 [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 gtable_0.1.2 [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 labeling_0.2 [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-29 Matrix_1.0-14 mclust_4.2 mgcv_1.7-26 [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 preprocessCore_1.22.0 [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 reshape_0.8.4 [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 zlibbioc_1.6.0 Thanks Juan --- Juan Fernandez Tajes, phD Grupo Xenomar ­ Área de Genética Facultad de Ciencias ­ A Zapateira Universidad de A Coruña Spain Tlf - +34 981 16700 Email: Jfernandezt@udc.es [[alternative HTML version deleted]]
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Hi Juan You need to try the latest developing version of methyAnalysis package. For some unknown reason, the Bioc reports some checking error of the vignette. So the latest developing version is not available through biocLite. It will send the package to you in another email. Thanks for reporting the problem! Pan On Tue, Nov 12, 2013 at 1:11 PM, jfertaj <jfernandezt@udc.es> wrote: > Dear list and Pan, > > I’m still having some problems with the methyAnalysis package, after > update some functions thanks to Pan I’m still experiencing some problems > with certain functions, for example I am not able to plot the heatmap with > > >heatmapByChromosome(methyGenoSet, gene='55342', > genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', includeGeneBody=TRUE) > Error in .local(range, ...) : could not find function "restoreSeqlevels" > Error: could not find function "restoreSeqlevels" > > or annotate the DMR regions with > > >DMRInfo.ann <- annotateDMRInfo(allDMRInfo, > 'TxDb.Hsapiens.UCSC.hg19.knownGene') > There were 50 or more warnings (use warnings() to see the first 50) > Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) : > error in evaluating the argument 'x' in selecting a method for function > 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), what = > c("sequence", : > sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, > chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, > chr21, chr22, chrX, chrY have incompatible genomes: > - in 'x': , , , , , , , , , , , , , , , , , , , , , , , > - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, > hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, > hg19, hg19 > > Here is my sessionInfo() > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] IlluminaHumanMethylation450k.db_2.0.7 > FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 > BSgenome_1.28.0 > [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 > plyr_1.8 pheatmap_0.7.7 > > [9] genefilter_1.42.0 multtest_2.18.0 > annotate_1.38.0 GOstats_2.26.0 > > [13] graph_1.38.3 Category_2.26.0 > IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 > > [17] lumi_2.14.0 methylumi_2.8.0 > matrixStats_0.8.5 ggplot2_0.9.3.1 > > [21] reshape2_1.2.2 scales_0.2.3 > methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 > > [25] RSQLite_0.11.4 DBI_0.2-7 > AnnotationDbi_1.22.6 Biobase_2.20.1 > > [29] GenomicRanges_1.12.4 IRanges_1.20.2 > BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 > base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 > biomaRt_2.16.0 > [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 > cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 > dichromat_2.0-0 > [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 > genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 > gtable_0.1.2 > [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 > iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 > labeling_0.2 > [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 > MASS_7.3-29 Matrix_1.0-14 mclust_4.2 > mgcv_1.7-26 > [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 > nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 > preprocessCore_1.22.0 > [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 > RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 > reshape_0.8.4 > [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 > rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 > [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 > XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 > zlibbioc_1.6.0 > > Thanks > > Juan > --- > Juan Fernandez Tajes, phD > Grupo Xenomar – Área de Genética > Facultad de Ciencias – A Zapateira > Universidad de A Coruña > Spain > Tlf - +34 981 16700 > Email: Jfernandezt@udc.es > > [[alternative HTML version deleted]]
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On 11/12/2013 11:11 PM, Pan Du wrote: > Hi Juan > > You need to try the latest developing version of methyAnalysis package. For > some unknown reason, the Bioc reports some checking error of the vignette. > So the latest developing version is not available through biocLite. It will > send the package to you in another email. Thanks for reporting the problem! Hi Pan -- update your installation and you'll be able to see the error; no sense distributing packages that don't work!. I introduced a change / bug in Biobase and will fix this today; the package should be available via biocLite tomorrow. Martin > > Pan > > > On Tue, Nov 12, 2013 at 1:11 PM, jfertaj <jfernandezt at="" udc.es=""> wrote: > >> Dear list and Pan, >> >> I?m still having some problems with the methyAnalysis package, after >> update some functions thanks to Pan I?m still experiencing some problems >> with certain functions, for example I am not able to plot the heatmap with >> >>> heatmapByChromosome(methyGenoSet, gene='55342', >> genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', includeGeneBody=TRUE) >> Error in .local(range, ...) : could not find function "restoreSeqlevels" >> Error: could not find function "restoreSeqlevels" >> >> or annotate the DMR regions with >> >> >DMRInfo.ann <- annotateDMRInfo(allDMRInfo, >> 'TxDb.Hsapiens.UCSC.hg19.knownGene') >> There were 50 or more warnings (use warnings() to see the first 50) >> Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) : >> error in evaluating the argument 'x' in selecting a method for function >> 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), what = >> c("sequence", : >> sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, >> chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, >> chr21, chr22, chrX, chrY have incompatible genomes: >> - in 'x': , , , , , , , , , , , , , , , , , , , , , , , >> - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >> hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >> hg19, hg19 >> >> Here is my sessionInfo() >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] parallel grid stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] IlluminaHumanMethylation450k.db_2.0.7 >> FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 >> BSgenome_1.28.0 >> [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 >> plyr_1.8 pheatmap_0.7.7 >> >> [9] genefilter_1.42.0 multtest_2.18.0 >> annotate_1.38.0 GOstats_2.26.0 >> >> [13] graph_1.38.3 Category_2.26.0 >> IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 >> >> [17] lumi_2.14.0 methylumi_2.8.0 >> matrixStats_0.8.5 ggplot2_0.9.3.1 >> >> [21] reshape2_1.2.2 scales_0.2.3 >> methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 >> >> [25] RSQLite_0.11.4 DBI_0.2-7 >> AnnotationDbi_1.22.6 Biobase_2.20.1 >> >> [29] GenomicRanges_1.12.4 IRanges_1.20.2 >> BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 >> base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 >> biomaRt_2.16.0 >> [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 >> cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 >> dichromat_2.0-0 >> [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 >> genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 >> gtable_0.1.2 >> [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 >> iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 >> labeling_0.2 >> [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 >> MASS_7.3-29 Matrix_1.0-14 mclust_4.2 >> mgcv_1.7-26 >> [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 >> nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 >> preprocessCore_1.22.0 >> [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 >> RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 >> reshape_0.8.4 >> [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 >> rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 >> stats4_3.0.2 >> [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 >> XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 >> zlibbioc_1.6.0 >> >> Thanks >> >> Juan >> --- >> Juan Fernandez Tajes, phD >> Grupo Xenomar ? ?rea de Gen?tica >> Facultad de Ciencias ? A Zapateira >> Universidad de A Coru?a >> Spain >> Tlf - +34 981 16700 >> Email: Jfernandezt at udc.es >> >> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Thanks! Martin The bugs are due to the changes of other depended packages. I have submitted the bug fix to the released version. Hope this will solve problems. Pan On Wed, Nov 13, 2013 at 7:29 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 11/12/2013 11:11 PM, Pan Du wrote: > >> Hi Juan >> >> You need to try the latest developing version of methyAnalysis package. >> For >> some unknown reason, the Bioc reports some checking error of the vignette. >> So the latest developing version is not available through biocLite. It >> will >> send the package to you in another email. Thanks for reporting the >> problem! >> > > Hi Pan -- update your installation and you'll be able to see the error; no > sense distributing packages that don't work!. I introduced a change / bug > in Biobase and will fix this today; the package should be available via > biocLite tomorrow. > > Martin > > >> Pan >> >> >> On Tue, Nov 12, 2013 at 1:11 PM, jfertaj <jfernandezt@udc.es> wrote: >> >> Dear list and Pan, >>> >>> I’m still having some problems with the methyAnalysis package, after >>> update some functions thanks to Pan I’m still experiencing some problems >>> with certain functions, for example I am not able to plot the heatmap >>> with >>> >>> heatmapByChromosome(methyGenoSet, gene='55342', >>>> >>> genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', >>> includeGeneBody=TRUE) >>> Error in .local(range, ...) : could not find function "restoreSeqlevels" >>> Error: could not find function "restoreSeqlevels" >>> >>> or annotate the DMR regions with >>> >>> >DMRInfo.ann <- annotateDMRInfo(allDMRInfo, >>> 'TxDb.Hsapiens.UCSC.hg19.knownGene') >>> There were 50 or more warnings (use warnings() to see the first 50) >>> Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) >>> : >>> error in evaluating the argument 'x' in selecting a method for >>> function >>> 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), >>> what = >>> c("sequence", : >>> sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, >>> chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, >>> chr21, chr22, chrX, chrY have incompatible genomes: >>> - in 'x': , , , , , , , , , , , , , , , , , , , , , , , >>> - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >>> hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >>> hg19, hg19 >>> >>> Here is my sessionInfo() >>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] parallel grid stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] IlluminaHumanMethylation450k.db_2.0.7 >>> FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 >>> BSgenome_1.28.0 >>> [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 >>> plyr_1.8 pheatmap_0.7.7 >>> >>> [9] genefilter_1.42.0 multtest_2.18.0 >>> annotate_1.38.0 GOstats_2.26.0 >>> >>> [13] graph_1.38.3 Category_2.26.0 >>> IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 >>> >>> [17] lumi_2.14.0 methylumi_2.8.0 >>> matrixStats_0.8.5 ggplot2_0.9.3.1 >>> >>> [21] reshape2_1.2.2 scales_0.2.3 >>> methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 >>> >>> [25] RSQLite_0.11.4 DBI_0.2-7 >>> AnnotationDbi_1.22.6 Biobase_2.20.1 >>> >>> [29] GenomicRanges_1.12.4 IRanges_1.20.2 >>> BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 >>> base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 >>> biomaRt_2.16.0 >>> [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 >>> cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 >>> dichromat_2.0-0 >>> [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 >>> genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 >>> gtable_0.1.2 >>> [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 >>> iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 >>> labeling_0.2 >>> [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 >>> MASS_7.3-29 Matrix_1.0-14 mclust_4.2 >>> mgcv_1.7-26 >>> [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 >>> nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 >>> preprocessCore_1.22.0 >>> [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 >>> RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 >>> reshape_0.8.4 >>> [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 >>> rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 >>> stats4_3.0.2 >>> [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 >>> XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 >>> zlibbioc_1.6.0 >>> >>> Thanks >>> >>> Juan >>> --- >>> Juan Fernandez Tajes, phD >>> Grupo Xenomar – Área de Genética >>> Facultad de Ciencias – A Zapateira >>> Universidad de A Coruña >>> Spain >>> Tlf - +34 981 16700 >>> Email: Jfernandezt@udc.es >>> >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
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