[BioC] Excluding probes during methylation analysis

[Victoria Svinti]

Hi there,

I decided to post after searching the forums for a few days, in hope that somebody can point me in the right direction. 

I am analysing a 450k methylation array to look for differentially methylated sites, and got as far as having normalised data. Various resources suggest that I need to drop probes with know SNPs residing in the sequence, microsattelites, those that anneal to multiple genomic locations etc. 

I have looked into the FDb.InfiniumMethylation.hg19 package (get450k), but I don't see the annotation regarding SNPs (could be due to my unfamiliarity with GRanges). I finally have acquired a list of these from the GEO, Illumina GPL13534, but wonder if it's outdated and if there is a better way of doing this. 

Does someone know of a good/any tutorial for this workflow?

Many thanks,
Victoria

--
Victoria Svinti
Colon Cancer Genetics Group
MRC Human Genetics Unit, IGMM
University of Edinburgh, Western General Hospital,
Crewe Road, Edinburgh, EH4 2XU


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