[BioC] Illumina BeadChips and beadarray

[Kellie J Archer/FS/VCU]

   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