Hi Matt and others, besides the expression chip, Illumina also has a bead chip for genome-wide methylation profiling (covering over 27000 CpG islands, mostly in promoter regions of ~13,000 well annotated human genes; same 12 arrays and 6 samples per chip). As opposed to the expression chip, this is a two-color system to interrogate both methylated and unmethylated status, and BeadStudio then computes an intensity ratio of each pair of probes. Next week I will get data from these methylation chips and it seems to me that I should also be able to process them using beadarray, do you agree? Has anyone out there done this already? Thanks, Ina

Ina, I have use the the beadarray package for processing data from Illumina's Methylation Cancer Panel I. The technology for interrogating the CpG sites is somewhat different from the HumanMethylation27 array, but still yields intensities from two channels. After reading in the data, I used createBeadSummaryData to get summaries for both the red and green channel and then performed background subtraction and formed the ratios myself. Hope that helps. Kellie J. Archer, Ph.D. Assistant Professor Department of Biostatistics & Massey Cancer Center Virginia Commonwealth University 730 East Broad St., 3-022 Richmond, VA 23298-0032 phone: (804) 827-2039 fax: (804) 828-8900 e-mail: [1]kjarcher at vcu.edu website: [2]www.people.vcu.edu/~kjarcher Message: 5 Date: Wed, 3 Sep 2008 15:39:44 -0400 (EDT) From: Ina Hoeschele <inah at="" vbi.vt.edu=""> Subject: Re: [BioC] Illumina BeadChips and beadarray To: Matt Ritchie <matt.ritchie at="" cancer.org.uk=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <191870519.485261220470784509.JavaMail.root at zimbra> Content-Type: text/plain; charset=utf-8 Hi Matt and others, besides the expression chip, Illumina also has a bead chip for genome-wide methylation profiling (covering over 27000 CpG islands, mostly in promoter regions of ~13,000 well annotated human genes; same 12 arrays and 6 samples per chip). As opposed to the expression chip, this is a two-color system to interrogate both methylated and unmethylated status, and BeadStudio then computes an intensity ratio of each pair of probes. Next week I will get data from these methylation chips and it seems to me that I should also be able to process them using beadarray, do you agree? Has anyone out there done this already? Thanks, Ina References 1. mailto:kjarcher at vcu.edu 2. http://www.people.vcu.edu/~kjarcher