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]]