[BioC] MEDME for MeDIP on Affymetrix promoter arrays

[mattia pelizzola]

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 at 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