Dear group, Is there a vignette on how to use MEDME for MeDIP based methylation profiling using Affymetrix promoter 1 chips. In the vignette provided in bioconductor directly talks about testMEDMEset, however I do not know what has to be done to process affymetrix data. all I have is CEL files and promoter 1 chip associated files. thank you. -Adrian

Hi Adrian, the MEDME set can be built following the instructions on the MEDME reference manual (available on the MEDME bioc web page http://www.bioconductor.org/packages/release/bioc/html/MEDME.html) or available typing class?MEDMEset on the R GUI once MEDME is installed. You need to use: newSet= new("MEDMEset", chr=CHRS, pos=POS, logR=LOGR) where CHRS, POS and LOGR correspond to what defined in that documentation So you need to extract chromosomal, position and logR for each probe on your array. I am not familiar with affy tiling arrays, but i am sure that there is some package here to deal with that. Alternatively you should have got some txt file from you affy service provider. Be careful that the logR is the log ratio between MeDIP and input DNA data. Each affy array has only one channel, so you need to combine and normalize different arrays to get this logR, the actual MeDIP enrichment. Finally, please remember that, as explained in the vignette, MEDME requires a calibration dataset based on a fully methylated sample. You can avoid that only if your dataset is highly enriched of fully methylated DNA. This is not the case for promoters. Best, mattia ---------- Forwarded message ---------- From: Adrian Johnson <oriolebaltimore@gmail.com> To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> Date: Thu, 2 Apr 2009 13:59:39 -0400 Subject: [BioC] MEDME for MeDIP on Affymetrix promoter arrays Dear group, Is there a vignette on how to use MEDME for MeDIP based methylation profiling using Affymetrix promoter 1 chips. In the vignette provided in bioconductor directly talks about testMEDMEset, however I do not know what has to be done to process affymetrix data. all I have is CEL files and promoter 1 chip associated files. thank you. -Adrian