[BioC] Methyl-Chip - Affymetrix promoter array

Hervé Pagès hpages at fhcrc.org
Thu Mar 26 02:30:23 CET 2009

Hi Adrian,

So you want us to tell whether you are doing the right thing by using
tools from others?  ;-)
The only thing I can suggest is that you try to intersect the genomic
regions by using our tools and compare the results (and the convenience)
with that of Galaxy. Rough steps to follow:
   (1) Install R + Bioconductor.
   (2) Install the rtracklayer package.
   (3) Import your bed files (with import.bed() or import.wig()) into
       UCSCData instances (x, y, etc...)
   (4) Load the IRanges package.
   (5) Extract the ranges from your UCSCData instances for chromosome
       'chrom' with something like 'ranges(x[chrom])'
   (6) Use the overlap() tool to intersect the ranges.


Adrian Johnson wrote:
> 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.
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
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E-mail: hpages at fhcrc.org
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