That is great, THANK YOU!
Hajja


--- On Mon, 8/1/11, Tim Triche, Jr. <ttriche@usc.edu> wrote:

From: Tim Triche, Jr. <ttriche@usc.edu>
Subject: Re: [BioC] Probe ID to Sequence
To: "Wong, Chao-Jen" <cwon2@fhcrc.org>
Cc: "bioconductor@r-project.org" <Bioconductor@r-project.org>, "khadeeja ismail" <hajjja@yahoo.com>
Date: Monday, August 1, 2011, 4:35 PM

nb.  The reason I mention this is that all problems of which I am aware are either marked as such (for problems which appear to be deeper than I am able to quickly address, such as RefGene:EntrezGene issues) or fixed (SNP, SNP10, STRAND, CPGS) in version 1.4.9 of the annotation package.



On Mon, Aug 1, 2011 at 4:33 PM, Tim Triche, Jr. <ttriche@usc.edu> wrote:


The 1.4.9 version of the package hadn't passed the build check due to a bizarre bug in R CMD check, but now that I'm running it again with a more recent (r56301) build of R and updated Bioconductor packages, it appears to be checking out fine.  I will re-upload it, but I would like to break the package into a lighter-weight annotations package and a heavier-weight probes package (with sequences instead of NuIDs) for the next real release.



I'll ask Marc for another FTP password and see about getting (at least) 1.4.9 uploaded shortly.

On Mon, Aug 1, 2011 at 4:20 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote:



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@gmail.com>

To: "Chao-Jen Wong" <cwon2@fhcrc.org>

Cc: "khadeeja ismail" <hajjja@yahoo.com>, bioconductor@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@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@yahoo.com >

To: bioconductor@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@fhcrc.org









_______________________________________________

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https://stat.ethz.ch/mailman/listinfo/bioconductor

Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor







--

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@fhcrc.org








-- 
When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes.



Derek Sivers








-- 
When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes.


Derek Sivers





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