problem with 'FDb.InfiniumMethylation.hg19'
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@james-w-macdonald-5106
Last seen 15 hours ago
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Hi Victoria, Please don't take conversations off-list (e.g., use Reply-all, instead of Reply when responding). We like to think of the list archives as a repository of knowledge, so making conversations private defeats that purpose. On 6/29/2013 4:11 PM, Victoria Svinti wrote: > Hi Jim, > > Thank you for your reply. I tried IlluminaHumanMethylation450k.db > first, but I get a warning message saying that it is deprecated, and > that I should use FDb.InfiniumMethylation.hg19 instead. Should I just > ignore that? Well, yes. The deprecation message comes from the IlluminaHumanMethylation450k.db package itself, and the package will become defunct at some point in time. And I assume that the lumi and in particular the methylumi packages will be updated in the interim to account for the deprecation of that package. But in the interim, you still need the IlluminaHumanMethylation450k.db package if you want to analyze your data using these packages. Best, Jim > > Much appreciated, > Vicky > > > On 28 Jun 2013, at 21:00, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > >> Hi Victoria, >> >> I think you want the IlluminaHumanMethylation450k.db package rather >> than the FDb package. >> >> Best, >> >> Jim >> >> On Jun 28, 2013 3:19 PM, "Victoria Svinti" >> <victoria.svinti at="" igmm.ed.ac.uk="">> <mailto:victoria.svinti at="" igmm.ed.ac.uk="">> wrote: >> >> Hi there, >> >> I came across another error when trying to load this annotation: >> >> obj <- lumiMethyR(fileName, lib="FDb.InfiniumMethylation.hg19") >> Error in get(paste(sub("\\.db$ <smb: .db$="">", "", lib), >> "COLORCHANNEL", sep = "")) : >> object 'FDb.InfiniumMethylation.hg19COLORCHANNEL' not found >> >> Does anyone else have this problem? Also, I still get the >> 'condition has length > 1 ?' error after downloading >> BSgenome.Hsapiens.UCSC.hg19... >> >> Would appreciate your thoughts. >> >> Thanks, >> Vicky >> >> ---- >> >> > sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] annotate_1.38.0 BiocInstaller_1.10.2 >> [3] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2 >> [5] Biostrings_2.28.0 GenomicFeatures_1.12.2 >> [7] AnnotationDbi_1.22.6 GenomicRanges_1.12.4 >> [9] IRanges_1.18.1 methylumi_2.6.1 >> [11] ggplot2_0.9.3.1 reshape2_1.2.2 >> [13] scales_0.2.3 lumi_2.12.0 >> [15] Biobase_2.20.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.38.1 affyio_1.28.0 >> [3] beanplot_1.1 biomaRt_2.16.0 >> [5] bitops_1.0-5 BSgenome_1.28.0 >> [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 colorspace_1.2-2 >> [9] DBI_0.2-7 dichromat_2.0-0 >> [11] digest_0.6.3 grid_3.0.0 >> [13] gtable_0.1.2 illuminaio_0.2.0 >> [15] KernSmooth_2.23-10 labeling_0.2 >> [17] lattice_0.20-15 limma_3.16.5 >> [19] MASS_7.3-26 Matrix_1.0-12 >> [21] matrixStats_0.8.1 mclust_4.1 >> [23] mgcv_1.7-24 minfi_1.6.0 >> [25] multtest_2.16.0 munsell_0.4 >> [27] nleqslv_2.0 nlme_3.1-109 >> [29] nor1mix_1.1-4 plyr_1.8 >> [31] preprocessCore_1.22.0 proto_0.3-10 >> [33] RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [35] reshape_0.8.4 R.methodsS3_1.4.2 >> [37] Rsamtools_1.12.3 RSQLite_0.11.4 >> [39] siggenes_1.34.0 splines_3.0.0 >> [41] stats4_3.0.0 stringr_0.6.2 >> [43] survival_2.37-4 tools_3.0.0 >> [45] XML_3.98-1.1 xtable_1.7-1 >> [47] zlibbioc_1.6.0 >> > >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> 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 >> > > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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VSM ▴ 120
@vsm-6019
Last seen 4.7 years ago
United Kingdom
Hi Jim, Thanks for tip re. posting. Good to know that it's safe to use IlluminaHumanMethylation450k.db for now. Best wishes, Victoria On 1 Jul 2013, at 14:53, James W. MacDonald <jmacdon at="" u.washington.edu=""> wrote: > Hi Victoria, > > Please don't take conversations off-list (e.g., use Reply-all, instead of Reply when responding). We like to think of the list archives as a repository of knowledge, so making conversations private defeats that purpose. > > On 6/29/2013 4:11 PM, Victoria Svinti wrote: >> Hi Jim, >> >> Thank you for your reply. I tried IlluminaHumanMethylation450k.db first, but I get a warning message saying that it is deprecated, and that I should use FDb.InfiniumMethylation.hg19 instead. Should I just ignore that? > > Well, yes. The deprecation message comes from the IlluminaHumanMethylation450k.db package itself, and the package will become defunct at some point in time. And I assume that the lumi and in particular the methylumi packages will be updated in the interim to account for the deprecation of that package. > > But in the interim, you still need the IlluminaHumanMethylation450k.db package if you want to analyze your data using these packages. > > Best, > > Jim > > >> >> Much appreciated, >> Vicky >> >> >> On 28 Jun 2013, at 21:00, James W. MacDonald <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">> wrote: >> >>> Hi Victoria, >>> >>> I think you want the IlluminaHumanMethylation450k.db package rather than the FDb package. >>> >>> Best, >>> >>> Jim >>> >>> On Jun 28, 2013 3:19 PM, "Victoria Svinti" <victoria.svinti at="" igmm.ed.ac.uk="" <mailto:victoria.svinti="" at="" igmm.ed.ac.uk="">> wrote: >>> >>> Hi there, >>> >>> I came across another error when trying to load this annotation: >>> >>> obj <- lumiMethyR(fileName, lib="FDb.InfiniumMethylation.hg19") >>> Error in get(paste(sub("\\.db$ <smb: .db$="">", "", lib), >>> "COLORCHANNEL", sep = "")) : >>> object 'FDb.InfiniumMethylation.hg19COLORCHANNEL' not found >>> >>> Does anyone else have this problem? Also, I still get the >>> 'condition has length > 1 ?' error after downloading >>> BSgenome.Hsapiens.UCSC.hg19... >>> >>> Would appreciate your thoughts. >>> >>> Thanks, >>> Vicky >>> >>> ---- >>> >>> > sessionInfo() >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets >>> methods >>> [8] base >>> >>> other attached packages: >>> [1] annotate_1.38.0 BiocInstaller_1.10.2 >>> [3] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2 >>> [5] Biostrings_2.28.0 GenomicFeatures_1.12.2 >>> [7] AnnotationDbi_1.22.6 GenomicRanges_1.12.4 >>> [9] IRanges_1.18.1 methylumi_2.6.1 >>> [11] ggplot2_0.9.3.1 reshape2_1.2.2 >>> [13] scales_0.2.3 lumi_2.12.0 >>> [15] Biobase_2.20.0 BiocGenerics_0.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.38.1 affyio_1.28.0 >>> [3] beanplot_1.1 biomaRt_2.16.0 >>> [5] bitops_1.0-5 BSgenome_1.28.0 >>> [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 colorspace_1.2-2 >>> [9] DBI_0.2-7 dichromat_2.0-0 >>> [11] digest_0.6.3 grid_3.0.0 >>> [13] gtable_0.1.2 illuminaio_0.2.0 >>> [15] KernSmooth_2.23-10 labeling_0.2 >>> [17] lattice_0.20-15 limma_3.16.5 >>> [19] MASS_7.3-26 Matrix_1.0-12 >>> [21] matrixStats_0.8.1 mclust_4.1 >>> [23] mgcv_1.7-24 minfi_1.6.0 >>> [25] multtest_2.16.0 munsell_0.4 >>> [27] nleqslv_2.0 nlme_3.1-109 >>> [29] nor1mix_1.1-4 plyr_1.8 >>> [31] preprocessCore_1.22.0 proto_0.3-10 >>> [33] RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> [35] reshape_0.8.4 R.methodsS3_1.4.2 >>> [37] Rsamtools_1.12.3 RSQLite_0.11.4 >>> [39] siggenes_1.34.0 splines_3.0.0 >>> [41] stats4_3.0.0 stringr_0.6.2 >>> [43] survival_2.37-4 tools_3.0.0 >>> [45] XML_3.98-1.1 xtable_1.7-1 >>> [47] zlibbioc_1.6.0 >>> > >>> >>> >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> 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 >>> >> >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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