[BioC] Application of Method of Aryee et al to Illumina methylation Arrays

[Martin Aryee]

Hi Rich,

The methods unfortunately wouldn't be suitable for Infinium arrays. The tools in this paper were developed using data from Roche (Nimblegen) microarrays and the McrBC restriction enzyme. Since the Illumina Infinium array is based on a completely different assay involving Bisulfite conversion, the methods wouldn't be applicable.

Best,
Martin.

Martin Aryee
Instructor
Dept. of Oncology/Biostatistics
Johns Hopkins University School of Medicine
aryee at jhu.edu
http://www.biostat.jhsph.edu/~maryee/


> From: Richard Friedman <friedman at cancercenter.columbia.edu>
> Date: January 23, 2011 3:42:24 PM EST
> To: bioconductor at r-project.org
> Subject: [BioC] Application of Method of Aryee et al to Illumina methylation Arrays
> 
> 
> Dear List,
> 
> 	Is it possible to apply the method described in
> 
> Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S,
> Irizarry RA. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics. 2010 Sep 27. [Epub ahead of print] PubMed  PMID: 20858772.
> 
> to Illumina Infinium methylation arrays?
> 
> Thanks and best wishes,
> Rich