On Wed, Jun 23, 2010 at 6:05 PM, Noemi Andor <Noemi.Andor@campus.lmu.de>wrote:

> Hello everybody,
>
> I'm currently working with Methylation data. Three data types:
> IlluminaDNAMethylation_OMA003_CPI_CPI,
> IlluminaDNAMethylation_OMA002_CPI_CPI
>
> both from Illumina Golden Gate BeadArray platform
>
> and
>
> Illumina Infinium Human DNA Methylation 27 platform
>
> After several trials, I finally succeeded loading the data into R(after
> reorganizing it into one single file - like in the example-data from the
> methylumi-package in R)
>
> But how do I get the mappings of the probe, e.g.
>
> Composite Element   Cy3                  Cy5    Detection Pvalue
> cg08367223      9.75030715328155        51.3125   3.68E-38
>
> Interpretation:   Cy5/Cy3 > 0 --> location x is hypermethylated,
>
> But where is this location x? Are there some mappings, similar to cdf-files
> from Affy-data, or is the location somehow encoded in the Composite element.
>
> The OMA003-platform for instance has comosites such as:
>
> SOX17_P303_F
>
> this means, it refers somehow to the SOX17 - gene, P303 - position 303
> starting from startcodon? F?
>
> would be very greatfull for some tipps.
>
>
For the Illumina 27k methylation platform, see:

http://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation27k.db.html

For the other two arrays, those appear to be custom OMAs, so you will want
to export the data from GenomeStudio including as much annotation as
possible.  Those annotation columns will end up as featureData in the
resulting MethyLumiSet object.

Sean

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