[BioC] Methyl-Chip - Affymetrix promoter array

[Adrian Johnson]

First: Apologies  since this is not directly R-Bioconductor related
question. Since many of you are actively involved in analyzing
MeDIP-chip data, I am asking on this platform. Sorry for brining
criticism.


Dear group,
I am analyzing MeDIP-Chip data. The enriched Me-DNA is hybridized to
Affymetrix human promoter 1 array.

I am using shirley Liu's MAT for identifying the peaks.  I got around
7K peaks of which I selected peaks with FDR with 2%.  The number of
probes is 3K.

I am using Galaxy to intersect regions.


Hs_PromP_NCBIv36.accession.unique.bed is a file that has genomic
coordinates in promoter regions of genes.
I am using Hs_PromP_NCBIv36.accession.unique.bed file  and BED file
from MAT to intersect genomic regions to obtain genes that belong to
enriched genomic regions.

I just want to make sure that is the correct procedure and using
Hs_PromP_NCBIv36.accession.unique.bed to intersect genomic regions and
getting list of methylated genes.

Again, please excuse me for out of context question. I appreciate any
members who can suggest.

thank you.
Adrian.