[BioC] Probe ID to Sequence

[Wong, Chao-Jen]

Good to know! Thanks!!! Wondering why they are not exported for they are important information for filtering purposes. 

Cheers,
Chao-Jen

----- Original Message -----
From: "Tim Triche, Jr." <tim.triche at gmail.com>
To: "Chao-Jen Wong" <cwon2 at fhcrc.org>
Cc: "khadeeja ismail" <hajjja at yahoo.com>, bioconductor at r-project.org
Sent: Monday, August 1, 2011 2:25:12 PM
Subject: Re: [BioC] Probe ID to Sequence

It's in there, simply not exported (d'oh!!!). IF need be you can use 



IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP 

IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10 

IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND 


to do these things. (I recognize that I am somewhat of a bad person for suggesting it, but it's the least of my sins) 


Note the handy abbreviations for minimal typing. 





On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen < cwon2 at fhcrc.org > wrote: 


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 




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If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. 

John von Neumann 

-- 
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