Dear list, We've noticed an apparent inconsistency in the bioc.db annotation file for the Illumina Human Methylation 450k arrays. IlluminaHumanMethylation450kCHR has some probes that aren't mapped to a chromosome but do have chromosomal locations Anyone using the 450K arrays will no doubt be running the development version of lumi in R-devel so I'm not sure if the .db annotation file has been updated but hasn't made it across to R-devel Eg x<- IlluminaHumanMethylation450kCHR # Get the probe identifiers that are mapped to a chromosome mapped_probes<- mappedkeys(x) # Convert to a list xx<- as.list(x[mapped_probes]) summary("cg00000165" %in% names(xx)) Mode FALSE NA's logical 1 0 but if I look at the files that come with 450 data, I can see cg00000165 is mapped to chr 1 Has anyone else encountered this? > sessionInfo() R version 2.14.0 Under development (unstable) (2011-07-02 r56248) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0 [3] RSQLite_0.9-4 DBI_0.2-5 [5] AnnotationDbi_1.15.9 lumi_2.5.1 [7] nleqslv_1.8.5 methylumi_1.9.0 [9] Biobase_2.13.7 David Martino Research Officer Cancer and Disease Epigenetics Murdoch Childrens Research Institute, Flemington Road Parkville VIC 3052 p 61 3 8341 6205 f 61 3 9348 1391 www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ [[alternative HTML version deleted]]

This is a result of CHR being derived from Entrez Gene mappings of accessions, while CHR37 (from Illumina's manifest v1.1) is from the hg19-aligned target sequence. I think the right thing to do is to clobber the Entrez Gene-derived version of CHR with the version from the Illumina manifest (CHR37) since, if a probe is not annotated to an EG ID, org.Hs.egCHR returns NA, thus IlluminaHumanMethylation450kCHR = NA. The expected behavior would instead be as implemented in CHR37. So the expeditious way to resolve this appears to be clobbering CHR with CHR37. I'll upload version 1.4.7 with this fix (and several others, such as exporting SNP and SNP10 maps) in the next few days. I had hoped that there was a more elegant solution to this and a couple of other issues related to accession mappings, but it is more important for the package to behave as expected than for it to be elegant. On Tue, Jul 5, 2011 at 4:41 PM, David Martino <david.martino@mcri.edu.au>wrote: > Dear list, > > > > We've noticed an apparent inconsistency in the bioc.db annotation file > for the Illumina Human Methylation 450k arrays. > > > > IlluminaHumanMethylation450kCHR has some probes that aren't mapped to a > chromosome but do have chromosomal locations > > > > Anyone using the 450K arrays will no doubt be running the development > version of lumi in R-devel so I'm not sure if the .db annotation file > has been updated but hasn't made it across to R-devel > > > > Eg > > > > x<- IlluminaHumanMethylation450kCHR > > # Get the probe identifiers that are mapped to a chromosome > > mapped_probes<- mappedkeys(x) > > # Convert to a list > > xx<- as.list(x[mapped_probes]) > > > > summary("cg00000165" %in% names(xx)) > > Mode FALSE NA's > > logical 1 0 > > > > but if I look at the files that come with 450 data, I can see > > cg00000165 is mapped to chr 1 > > > > > > Has anyone else encountered this? > > > > > sessionInfo() > > > R version 2.14.0 Under development (unstable) (2011-07-02 r56248) > > > 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=C LC_NAME=C > > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > other attached packages: > > > [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0 > > > [3] RSQLite_0.9-4 DBI_0.2-5 > > > > [5] AnnotationDbi_1.15.9 lumi_2.5.1 > > > > [7] nleqslv_1.8.5 methylumi_1.9.0 > > > > [9] Biobase_2.13.7 > > > > > > > > > > > David Martino > > Research Officer > > Cancer and Disease Epigenetics > > Murdoch Childrens Research Institute, > > Flemington Road Parkville VIC 3052 > > > > p 61 3 8341 6205 f 61 3 9348 1391 www.mcri.edu.au > > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ > [[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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

Dear All, I have analyzed a time course microarray data (4 time points). I am interested in genes which are significantly differentially expressed at all 4 time points. Can TukeyHSD or some other post-hoc test be performed in limma? Could another strategy be used to achieve what I want? Thank you. -Sohail -----bioconductor-bounces at r-project.org wrote: ----- To: <bioconductor at="" r-project.org=""> From: "David Martino" Sent by: bioconductor-bounces at r-project.org Date: 07/05/2011 07:42PM Subject: [BioC] inconsistent CHR mapping- IlluminaHumanMethylation450k.db Dear list, We've noticed an apparent inconsistency in the bioc.db annotation file for the Illumina Human Methylation 450k arrays. IlluminaHumanMethylation450kCHR has some probes that aren't mapped to a chromosome but do have chromosomal locations Anyone using the 450K arrays will no doubt be running the development version of lumi in R-devel so I'm not sure if the .db annotation file has been updated but hasn't made it across to R-devel Eg x<- IlluminaHumanMethylation450kCHR # Get the probe identifiers that are mapped to a chromosome mapped_probes<- mappedkeys(x) # Convert to a list xx<- as.list(x[mapped_probes]) summary("cg00000165" %in% names(xx)) Mode FALSE NA's logical 1 0 but if I look at the files that come with 450 data, I can see cg00000165 is mapped to chr 1 Has anyone else encountered this? > sessionInfo() R version 2.14.0 Under development (unstable) (2011-07-02 r56248) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0 [3] RSQLite_0.9-4 DBI_0.2-5 [5] AnnotationDbi_1.15.9 lumi_2.5.1 [7] nleqslv_1.8.5 methylumi_1.9.0 [9] Biobase_2.13.7 David Martino Research Officer Cancer and Disease Epigenetics Murdoch Childrens Research Institute, Flemington Road Parkville VIC 3052 p 61 3 8341 6205 f 61 3 9348 1391 www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit [1]http://www.messagelabs.com/email ______________________________________________________________________ [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org [2]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [3]http://news.gmane.org/gmane.science.biology.informatics.conductor References 1. http://www.messagelabs.com/email 2. https://stat.ethz.ch/mailman/listinfo/bioconductor 3. http://news.gmane.org/gmane.science.biology.informatics.conductor