## 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/>
>
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>
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-- 
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>

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