error on loading ratioConvert() in minfi
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Dear Users, I tried to convert the set to ratioset using ratioConvert(), but it has an error message > ratioConvert(RGset, what = c("beta", "M", "both"), keepCN = TRUE) Error: could not find function "ratioConvert" I installed minfi and load the library, I don't get it why this error message coming out? Thanks, -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] FDb.UCSC.snp137common.hg19_1.0.0 [2] GenomicFeatures_1.12.4 [3] IlluminaHumanMethylation450k.db_2.0.7 [4] org.Hs.eg.db_2.9.0 [5] RSQLite_0.11.4 [6] DBI_0.2-7 [7] AnnotationDbi_1.22.6 [8] minfiData_0.3.4 [9] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3 [10] IlluminaHumanMethylation450kmanifest_0.4.0 [11] methylumi_2.6.1 [12] ggplot2_0.9.3.1 [13] reshape2_1.4 [14] scales_0.2.4 [15] lumi_2.12.0 [16] minfi_1.6.0 [17] Biostrings_2.28.0 [18] GenomicRanges_1.12.5 [19] IRanges_1.18.4 [20] reshape_0.8.5 [21] lattice_0.20-29 [22] Biobase_2.22.0 [23] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 [4] beanplot_1.1 BiocInstaller_1.10.4 biomaRt_2.16.0 [7] bitops_1.0-6 BSgenome_1.28.0 colorspace_1.2-4 [10] digest_0.6.4 grid_3.0.3 gtable_0.1.2 [13] illuminaio_0.2.0 KernSmooth_2.23-12 limma_3.16.8 [16] MASS_7.3-33 Matrix_1.1-3 matrixStats_0.8.14 [19] mclust_4.3 mgcv_1.7-29 multtest_2.16.0 [22] munsell_0.4.2 nleqslv_2.1.1 nlme_3.1-117 [25] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.22.0 [28] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 [31] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.12.4 [34] rtracklayer_1.20.4 siggenes_1.34.0 splines_3.0.3 [37] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 [40] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 [43] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
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@kasper-daniel-hansen-2979
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Upgrade, minfi 1.6.0 is ancient. Kasper On Wed, May 21, 2014 at 11:45 AM, guest [guest] <guest@bioconductor.org>wrote: > Dear Users, > > I tried to convert the set to ratioset using ratioConvert(), but it has an > error message > > > ratioConvert(RGset, what = c("beta", "M", "both"), keepCN = TRUE) > Error: could not find function "ratioConvert" > > I installed minfi and load the library, I don't get it why this error > message coming out? > > Thanks, > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.3 (2014-03-06) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] FDb.UCSC.snp137common.hg19_1.0.0 > [2] GenomicFeatures_1.12.4 > [3] IlluminaHumanMethylation450k.db_2.0.7 > [4] org.Hs.eg.db_2.9.0 > [5] RSQLite_0.11.4 > [6] DBI_0.2-7 > [7] AnnotationDbi_1.22.6 > [8] minfiData_0.3.4 > [9] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3 > [10] IlluminaHumanMethylation450kmanifest_0.4.0 > [11] methylumi_2.6.1 > [12] ggplot2_0.9.3.1 > [13] reshape2_1.4 > [14] scales_0.2.4 > [15] lumi_2.12.0 > [16] minfi_1.6.0 > [17] Biostrings_2.28.0 > [18] GenomicRanges_1.12.5 > [19] IRanges_1.18.4 > [20] reshape_0.8.5 > [21] lattice_0.20-29 > [22] Biobase_2.22.0 > [23] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 > [4] beanplot_1.1 BiocInstaller_1.10.4 biomaRt_2.16.0 > [7] bitops_1.0-6 BSgenome_1.28.0 colorspace_1.2-4 > [10] digest_0.6.4 grid_3.0.3 gtable_0.1.2 > [13] illuminaio_0.2.0 KernSmooth_2.23-12 limma_3.16.8 > [16] MASS_7.3-33 Matrix_1.1-3 matrixStats_0.8.14 > [19] mclust_4.3 mgcv_1.7-29 multtest_2.16.0 > [22] munsell_0.4.2 nleqslv_2.1.1 nlme_3.1-117 > [25] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.22.0 > [28] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 > [31] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.12.4 > [34] rtracklayer_1.20.4 siggenes_1.34.0 splines_3.0.3 > [37] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 > [40] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 > [43] zlibbioc_1.6.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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Hi Kasper, We just upgraded to version 1.10.0, but it still doesn't work. > library(minfi) > ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), keepCN = TRUE) Error: could not find function "ratioConvert" Thanks, Li From: Kasper Daniel Hansen <khansen@jhsph.edu<mailto:khansen@jhsph.edu>> Date: Wed, 21 May 2014 13:33:54 -0400 To: "guest [guest]" <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> Cc: "bioconductor at r-project.org<mailto:bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org<mailto:bioconductor="" at="" r-project.org="">>, "Jia, Li (NIH/NCI) [C]" <jial2 at="" mail.nih.gov<mailto:jial2="" at="" mail.nih.gov="">> Subject: Re: [BioC] error on loading ratioConvert() in minfi Upgrade, minfi 1.6.0 is ancient. Kasper On Wed, May 21, 2014 at 11:45 AM, guest [guest] <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> wrote: Dear Users, I tried to convert the set to ratioset using ratioConvert(), but it has an error message > ratioConvert(RGset, what = c("beta", "M", "both"), keepCN = TRUE) Error: could not find function "ratioConvert" I installed minfi and load the library, I don't get it why this error message coming out? Thanks, -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] FDb.UCSC.snp137common.hg19_1.0.0 [2] GenomicFeatures_1.12.4 [3] IlluminaHumanMethylation450k.db_2.0.7 [4] org.Hs.eg.db_2.9.0 [5] RSQLite_0.11.4 [6] DBI_0.2-7 [7] AnnotationDbi_1.22.6 [8] minfiData_0.3.4 [9] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3 [10] IlluminaHumanMethylation450kmanifest_0.4.0 [11] methylumi_2.6.1 [12] ggplot2_0.9.3.1 [13] reshape2_1.4 [14] scales_0.2.4 [15] lumi_2.12.0 [16] minfi_1.6.0 [17] Biostrings_2.28.0 [18] GenomicRanges_1.12.5 [19] IRanges_1.18.4 [20] reshape_0.8.5 [21] lattice_0.20-29 [22] Biobase_2.22.0 [23] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 [4] beanplot_1.1 BiocInstaller_1.10.4 biomaRt_2.16.0 [7] bitops_1.0-6 BSgenome_1.28.0 colorspace_1.2-4 [10] digest_0.6.4 grid_3.0.3 gtable_0.1.2 [13] illuminaio_0.2.0 KernSmooth_2.23-12 limma_3.16.8 [16] MASS_7.3-33 Matrix_1.1-3 matrixStats_0.8.14 [19] mclust_4.3 mgcv_1.7-29 multtest_2.16.0 [22] munsell_0.4.2 nleqslv_2.1.1 nlme_3.1-117 [25] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.22.0 [28] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 [31] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.12.4 [34] rtracklayer_1.20.4 siggenes_1.34.0 splines_3.0.3 [37] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 [40] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 [43] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Wed, May 21, 2014 at 1:59 PM, Jia, Li (NIH/NCI) [C] <li.jia2@nih.gov>wrote: > library(minfi) > > ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), > keepCN = TRUE) > Well, it works fine for me. Perhaps look at sessionInfo() after error and verify you're on a new minfi version. > library(minfiData) > ratioSet <- ratioConvert(MsetEx, what = c("beta", "M", "both"), keepCN = TRUE) > sessionInfo() R version 3.1.0 Patched (2014-04-26 r65503) Platform: x86_64-apple-darwin13.1.0 (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] minfiData_0.6.0 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [3] IlluminaHumanMethylation450kmanifest_0.4.0 [4] minfi_1.10.1 [5] bumphunter_1.4.0 [6] locfit_1.5-9.1 [7] iterators_1.0.7 [8] foreach_1.4.2 [9] Biostrings_2.32.0 [10] XVector_0.4.0 [11] GenomicRanges_1.16.3 [12] GenomeInfoDb_1.0.2 [13] IRanges_1.22.6 [14] lattice_0.20-29 [15] Biobase_2.24.0 [16] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1 [4] beanplot_1.1 codetools_0.2-8 DBI_0.2-7 [7] digest_0.6.4 doRNG_1.6 genefilter_1.46.0 [10] grid_3.1.0 illuminaio_0.6.0 limma_3.20.1 [13] MASS_7.3-31 matrixStats_0.8.14 mclust_4.3 [16] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 [19] pkgmaker_0.20 plyr_1.8.1 preprocessCore_1.26.0 [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 [25] registry_0.2 reshape_0.8.5 rngtools_1.2.4 [28] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 [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] zlibbioc_1.10.0 [[alternative HTML version deleted]]
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Hi Kasper, You are right, I restarted the new session, it works. But when I tried to move along the analysis to generate the GenomeratioSet, it has another error message: > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: range cannot be determined from the supplied arguments (too many NAs) Could you please let me know what's wrong with this? Thanks a lot, Li From: Kasper Daniel Hansen <khansen@jhsph.edu<mailto:khansen@jhsph.edu>> Date: Thu, 22 May 2014 22:23:48 -0400 To: "Jia, Li (NIH/NCI) [C]" <li.jia2 at="" nih.gov<mailto:li.jia2="" at="" nih.gov="">> Cc: "guest [guest]" <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">>, "bioconductor at r-project.org<mailto:bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org<mailto:bioconductor="" at="" r-project.org="">> Subject: Re: [BioC] error on loading ratioConvert() in minfi On Wed, May 21, 2014 at 1:59 PM, Jia, Li (NIH/NCI) [C] <li.jia2 at="" nih.gov<mailto:li.jia2="" at="" nih.gov="">> wrote: library(minfi) > ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), keepCN = TRUE) Well, it works fine for me. Perhaps look at sessionInfo() after error and verify you're on a new minfi version. > library(minfiData) > ratioSet <- ratioConvert(MsetEx, what = c("beta", "M", "both"), keepCN = TRUE) > sessionInfo() R version 3.1.0 Patched (2014-04-26 r65503) Platform: x86_64-apple-darwin13.1.0 (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] minfiData_0.6.0 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [3] IlluminaHumanMethylation450kmanifest_0.4.0 [4] minfi_1.10.1 [5] bumphunter_1.4.0 [6] locfit_1.5-9.1 [7] iterators_1.0.7 [8] foreach_1.4.2 [9] Biostrings_2.32.0 [10] XVector_0.4.0 [11] GenomicRanges_1.16.3 [12] GenomeInfoDb_1.0.2 [13] IRanges_1.22.6 [14] lattice_0.20-29 [15] Biobase_2.24.0 [16] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1 [4] beanplot_1.1 codetools_0.2-8 DBI_0.2-7 [7] digest_0.6.4 doRNG_1.6 genefilter_1.46.0 [10] grid_3.1.0 illuminaio_0.6.0 limma_3.20.1 [13] MASS_7.3-31 matrixStats_0.8.14 mclust_4.3 [16] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 [19] pkgmaker_0.20 plyr_1.8.1 preprocessCore_1.26.0 [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 [25] registry_0.2 reshape_0.8.5 rngtools_1.2.4 [28] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 [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] zlibbioc_1.10.0
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