Processing of Illumina Infinium methylation microarray data using lumi - addColorChannelInfo bug?
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Paolo Sonego ▴ 140
@paolo-sonego-3256
Last seen 8.4 years ago
Italy
Hi guys, I'm trying to analyze some Illumina Infinium methylation microarray data using the new lumi package (btw, great improvement and nice brand new methylation vignette). The following error is produced when trying to replicate the example in the addColorChannelInfo() manual > ?addColorChannelInfo > data(example.lumiMethy) > head(pData(featureData(example.lumiMethy))) CHR COLOR_CHANNEL cg00002426 3 Red cg00012386 1 Red cg00013618 22 Grn cg00014837 12 Red cg00020533 6 Red cg00021527 17 Red > # removing color channel information > testData = example.lumiMethy > pData(featureData(testData))$COLOR_CHANNEL = NULL > testData = addColorChannelInfo(testData, lib="IlluminaHumanMethylation27k.db") Loading required package: IlluminaHumanMethylation27k.db Loading required package: AnnotationDbi Loading required package: org.Hs.eg.db Loading required package: DBI Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = "")) : object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found > # check whether the color channel information is added > head(pData(featureData(testData))) CHR cg00002426 3 cg00012386 1 cg00013618 22 cg00014837 12 cg00020533 6 cg00021527 17 Is this a bug? Any help would be appreciated! Thanks! Paolo Here is the output of my sessionInfo(): > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.5 [3] RSQLite_0.9-2 DBI_0.2-5 [5] AnnotationDbi_1.12.0 lumi_2.2.0 [7] Biobase_2.10.0 fortunes_1.4-0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 [4] grid_2.12.0 hdrcde_2.14 KernSmooth_2.23-4 [7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44 [10] methylumi_1.4.0 mgcv_1.6-2 nlme_3.1-97 [13] preprocessCore_1.12.0 tools_2.12.0 xtable_1.5-6
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@sean-davis-490
Last seen 5 months ago
United States
On Wed, Oct 20, 2010 at 8:33 AM, Paolo Sonego <paolo.sonego@gmail.com>wrote: > Hi guys, > I'm trying to analyze some Illumina Infinium methylation microarray data > using the new lumi package (btw, great improvement and nice brand new > methylation vignette). > The following error is produced when trying to replicate the example in > the addColorChannelInfo() manual > > ?addColorChannelInfo > > data(example.lumiMethy) > > head(pData(featureData(example.lumiMethy))) > CHR COLOR_CHANNEL > cg00002426 3 Red > cg00012386 1 Red > cg00013618 22 Grn > cg00014837 12 Red > cg00020533 6 Red > cg00021527 17 Red > > # removing color channel information > > testData = example.lumiMethy > > pData(featureData(testData))$COLOR_CHANNEL = NULL > > testData = addColorChannelInfo(testData, > lib="IlluminaHumanMethylation27k.db") > Loading required package: IlluminaHumanMethylation27k.db > Loading required package: AnnotationDbi > Loading required package: org.Hs.eg.db > Loading required package: DBI > Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = "")) : > object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found > > # check whether the color channel information is added > > head(pData(featureData(testData))) > CHR > cg00002426 3 > cg00012386 1 > cg00013618 22 > cg00014837 12 > cg00020533 6 > cg00021527 17 > > > Is this a bug? > Any help would be appreciated! > Thanks! > > Paolo > > Here is the output of my sessionInfo(): > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.5 > Hi, Paolo. You have some mismatches between the version of Bioconductor and the packages listed here. You will need to upgrade at least the IlluminaHumanMethylation27k.db to version 1.4.0, the version for Bioc 2.7 and R 2.12. Sean > [3] RSQLite_0.9-2 DBI_0.2-5 > [5] AnnotationDbi_1.12.0 lumi_2.2.0 > [7] Biobase_2.10.0 fortunes_1.4-0 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 > [4] grid_2.12.0 hdrcde_2.14 KernSmooth_2.23-4 > [7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44 > [10] methylumi_1.4.0 mgcv_1.6-2 nlme_3.1-97 > [13] preprocessCore_1.12.0 tools_2.12.0 xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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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Dear Sean, Thanks for the quick and effective solution! My problem was I previously installed the IlluminaHumanMethylation27k.db using the standard procedure: > source("http://bioconductor.org/biocLite.R") > biocLite("IlluminaHumanMethylation27k.db") Unfortunately on the release repository (http://www.bioconductor.org/packages/release/data/annotation/html/Ill uminaHumanMethylation27k.db.html) you can find only the IlluminaHumanMethylation27k.db_1.2.0.tgz binary package for Mac OS X 10.5. Installing from the package source using the good old: R CMD INSTALL IlluminaHumanMethylation27k.db_1.4.0.tar.gz solved the problems. Thanks again! Paolo On 10/20/10 2:51 PM, Sean Davis wrote: > > > On Wed, Oct 20, 2010 at 8:33 AM, Paolo Sonego <paolo.sonego@gmail.com> <mailto:paolo.sonego@gmail.com>> wrote: > > Hi guys, > I'm trying to analyze some Illumina Infinium methylation > microarray data using the new lumi package (btw, great improvement > and nice brand new methylation vignette). > The following error is produced when trying to replicate the > example in the addColorChannelInfo() manual > > ?addColorChannelInfo > > data(example.lumiMethy) > > head(pData(featureData(example.lumiMethy))) > CHR COLOR_CHANNEL > cg00002426 3 Red > cg00012386 1 Red > cg00013618 22 Grn > cg00014837 12 Red > cg00020533 6 Red > cg00021527 17 Red > > # removing color channel information > > testData = example.lumiMethy > > pData(featureData(testData))$COLOR_CHANNEL = NULL > > testData = addColorChannelInfo(testData, > lib="IlluminaHumanMethylation27k.db") > Loading required package: IlluminaHumanMethylation27k.db > Loading required package: AnnotationDbi > Loading required package: org.Hs.eg.db > Loading required package: DBI > Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = > "")) : > object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found > > # check whether the color channel information is added > > head(pData(featureData(testData))) > CHR > cg00002426 3 > cg00012386 1 > cg00013618 22 > cg00014837 12 > cg00020533 6 > cg00021527 17 > > > Is this a bug? > Any help would be appreciated! > Thanks! > > Paolo > > Here is the output of my sessionInfo(): > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.5 > > > Hi, Paolo. You have some mismatches between the version of > Bioconductor and the packages listed here. You will need to upgrade > at least the IlluminaHumanMethylation27k.db to version 1.4.0, the > version for Bioc 2.7 and R 2.12. > > Sean > > [3] RSQLite_0.9-2 DBI_0.2-5 > [5] AnnotationDbi_1.12.0 lumi_2.2.0 > [7] Biobase_2.10.0 fortunes_1.4-0 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 > [4] grid_2.12.0 hdrcde_2.14 KernSmooth_2.23-4 > [7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44 > [10] methylumi_1.4.0 mgcv_1.6-2 nlme_3.1-97 > [13] preprocessCore_1.12.0 tools_2.12.0 xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> > 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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On Wed, Oct 20, 2010 at 9:05 AM, Paolo Sonego <paolo.sonego@gmail.com>wrote: > Dear Sean, > Thanks for the quick and effective solution! > My problem was I previously installed the IlluminaHumanMethylation27k.db > using the standard procedure: > > > source("http://bioconductor.org/biocLite.R") > > biocLite("IlluminaHumanMethylation27k.db") > Unfortunately on the release repository > ( > http://www.bioconductor.org/packages/release/data/annotation/html/Il luminaHumanMethylation27k.db.html > ) > you can find only the IlluminaHumanMethylation27k.db_1.2.0.tgz > binary package for Mac OS X 10.5. > That is a problem. We'll have to fix that. Sean > Installing from the package source using the good old: > > R CMD INSTALL IlluminaHumanMethylation27k.db_1.4.0.tar.gz > > solved the problems. > > Thanks again! > > Paolo > > On 10/20/10 2:51 PM, Sean Davis wrote: > > > > > > On Wed, Oct 20, 2010 at 8:33 AM, Paolo Sonego <paolo.sonego@gmail.com> > <mailto:paolo.sonego@gmail.com>> wrote: > > > > Hi guys, > > I'm trying to analyze some Illumina Infinium methylation > > microarray data using the new lumi package (btw, great improvement > > and nice brand new methylation vignette). > > The following error is produced when trying to replicate the > > example in the addColorChannelInfo() manual > > > ?addColorChannelInfo > > > data(example.lumiMethy) > > > head(pData(featureData(example.lumiMethy))) > > CHR COLOR_CHANNEL > > cg00002426 3 Red > > cg00012386 1 Red > > cg00013618 22 Grn > > cg00014837 12 Red > > cg00020533 6 Red > > cg00021527 17 Red > > > # removing color channel information > > > testData = example.lumiMethy > > > pData(featureData(testData))$COLOR_CHANNEL = NULL > > > testData = addColorChannelInfo(testData, > > lib="IlluminaHumanMethylation27k.db") > > Loading required package: IlluminaHumanMethylation27k.db > > Loading required package: AnnotationDbi > > Loading required package: org.Hs.eg.db > > Loading required package: DBI > > Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = > > "")) : > > object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found > > > # check whether the color channel information is added > > > head(pData(featureData(testData))) > > CHR > > cg00002426 3 > > cg00012386 1 > > cg00013618 22 > > cg00014837 12 > > cg00020533 6 > > cg00021527 17 > > > > > > Is this a bug? > > Any help would be appreciated! > > Thanks! > > > > Paolo > > > > Here is the output of my sessionInfo(): > > > sessionInfo() > > R version 2.12.0 (2010-10-15) > > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.5 > > > > > > Hi, Paolo. You have some mismatches between the version of > > Bioconductor and the packages listed here. You will need to upgrade > > at least the IlluminaHumanMethylation27k.db to version 1.4.0, the > > version for Bioc 2.7 and R 2.12. > > > > Sean > > > > [3] RSQLite_0.9-2 DBI_0.2-5 > > [5] AnnotationDbi_1.12.0 lumi_2.2.0 > > [7] Biobase_2.10.0 fortunes_1.4-0 > > > > loaded via a namespace (and not attached): > > [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 > > [4] grid_2.12.0 hdrcde_2.14 KernSmooth_2.23-4 > > [7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44 > > [10] methylumi_1.4.0 mgcv_1.6-2 nlme_3.1-97 > > [13] preprocessCore_1.12.0 tools_2.12.0 xtable_1.5-6 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch <mailto:> Bioconductor@stat.math.ethz.ch> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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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