[BioC] Probe ID to Sequence

[Wong, Chao-Jen]

Hi, Khadeeja,

Accession number and regulatory group can be found in IlluminaHumanMethylation450k.db.  Unfortunately this database package does not have snp10. The easiest way I found is exporting those information (snp10 and UCSC refname) along with the probe intensity data from GenomeStudio. If anyone has better solution, please let me know. 

As for for snp probes, you can easily tell from the probe IDs as snp probe ID always start with rsxxxx. 


Cheers,
Chao-Jen

----- Original Message -----
From: "khadeeja ismail" <hajjja at yahoo.com>
To: bioconductor at r-project.org
Sent: Monday, August 1, 2011 1:25:54 AM
Subject: Re: [BioC] Probe ID to Sequence

Hi,

I need to find the following information for my IlluminaHumanMethylation450k probes but have no clue which packages I need.

--Probe SNPs, SNP10
--UCSC refgene name, group and accession number.

I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges, GenomicFeatures as any related packages, but cannot see how I can use these. 

Any help is most appreciated.

Best Regards,
Hajja

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-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org