Chromosome information in MethyLumiM object
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@francesco-mancuso-4483
Last seen 8.4 years ago
Hi group! I'm doing an analysis of methylation data from the Illumina Infinium 27K Methylation array using the /lumi/ package. I need to associate the CpGs with the respective chromosome. Does anyone know how to integrate the information about the chromosomes in a MethyLumiM object? Many thanks in advance, Francesco -- *Francesco Mattia Mancuso* - Bioinformatician at Bioinformatics Core Facility - Bioinformatician at Proteomics Core Facility CRG-Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Telephone: +34 933160202 francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> [[alternative HTML version deleted]]
Proteomics Proteomics • 581 views
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 2.4 years ago
United States
## AML is a MethyLumiM object; ## fData(AML) is its featureData > library(IlluminaHumanMethylation27k.db) > fData(AML)$chrom<- as.factor(unlist(mget(featureNames(AML), IlluminaHumanMethylation27kCHR))) > table(fData(AML)$chrom) 1 10 11 12 13 14 15 16 17 18 19 2287 848 1315 1268 399 684 643 900 1275 313 1449 2 20 21 22 3 4 5 6 7 8 9 1384 662 235 494 1255 830 955 1239 939 772 829 X Y 2 4 There are some NAs in the IlluminaHumanMethylation27k.db release currently available; I'll see about fixing those in the very near future, although it should be noted that there are a number of duplicates, repetitive sequences, and similarly undesirable bits in the 27k probes. It's up to the user to weed out the probes they don't want in that respect. --t On Fri, Feb 11, 2011 at 4:18 AM, Francesco Mancuso <francesco.mancuso@crg.eu> wrote: > Hi group! > I'm doing an analysis of methylation data from the Illumina Infinium 27K > Methylation array using the /lumi/ package. > I need to associate the CpGs with the respective chromosome. > > Does anyone know how to integrate the information about the chromosomes > in a MethyLumiM object? > > Many thanks in advance, > Francesco > > > -- > > *Francesco Mattia Mancuso* > - Bioinformatician at Bioinformatics Core Facility > - Bioinformatician at Proteomics Core Facility > > CRG-Centre for Genomic Regulation > C/ Dr. Aiguader, 88 > Edif. PRBB > 08003 Barcelona, Spain > > Telephone: +34 933160202 > francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> > www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> > > [[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]]