[BioC] methylumi

Noemi Andor Noemi.Andor at campus.lmu.de
Thu Jun 24 00:05:49 CEST 2010

Hello everybody,

I'm currently working with Methylation data. Three data types:

both from Illumina Golden Gate BeadArray platform 


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:


this means, it refers somehow to the SOX17 - gene, P303 - position 303 starting from startcodon? F?

would be very greatfull for some tipps.



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