[Fwd: help in annotation ILLUMINA probes]
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nac ▴ 280
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Dear all, I have a set of probes Ids from illumina beads arrays illuminaProbeID ILMN_1250814 ILMN_1257855 ILMN_2537948 ILMN_3144164 ILMN_2636200 what is the best way to fetch the chromosomal location of those ( chr: start :end)? Many thanks Nathalie -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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Mete Civelek ▴ 180
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Illumina has this information on their manifest files for each beadchip. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Nathalie Conte Sent: Monday, May 16, 2011 10:14 AM To: Bioconductor mailing list Subject: [BioC] [Fwd: help in annotation ILLUMINA probes] Dear all, I have a set of probes Ids from illumina beads arrays illuminaProbeID ILMN_1250814 ILMN_1257855 ILMN_2537948 ILMN_3144164 ILMN_2636200 what is the best way to fetch the chromosomal location of those ( chr: start :end)? Many thanks Nathalie -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor IMPORTANT WARNING: This email (and any attachments) is ...{{dropped:9}}
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Hi Nathalie, You can use the illumina Bioconductor annotation packages to do this. The particular one you need is illuminaMousev2.db >library(illuminaMousev2.db) > ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164", "ILMN_2636200") > mget(ids, illuminaMousev2GENOMICLOCATION) $ILMN_1250814 [1] "chr9:53240676:53240725:+" $ILMN_1257855 [1] "chrX:96269326:96269375:+" $ILMN_2537948 [1] "chr6:68192672:68192721:+" $ILMN_3144164 [1] "chr8:11004508:11004557:-" $ILMN_2636200 [1] "chr10:5324478:5324527:+" The coordinates are based on the mm9 assembly. You can also retrieve the probe sequences themselves in a similar technique. > mget(ids, illuminaMousev2PROBESEQUENCE) $ILMN_1250814 [1] "GGATTCCCTTTTCTGAGCGATGGACCTACCTTCAAGCCCACTTTCCAGCG" $ILMN_1257855 [1] "CCTCATGCCTTTTGCCTACAGTGGTGGTCTATAAGAACAGTCCTTTTGGC" $ILMN_2537948 [1] "GGGCAAGGACCACAGCCAACTTCCTCTTACAAGCCACACCGACTTTGTCC" $ILMN_3144164 [1] "CCAGGCACTGGAGCTTTGCCCTCTGCCAGCACCTATGCAAGCATCGACTT" $ILMN_2636200 [1] "TTTGCCCGATCCTTCCATCCGATGCTCAGATATACCAACGGTCCTCCTCC" Running the following will list all available mappings in the package. > illuminaMousev2() Best wishes, Mark On Mon, May 16, 2011 at 6:44 PM, Mete Civelek <mcivelek at="" mednet.ucla.edu=""> wrote: > Illumina has this information on their manifest files for each beadchip. > > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of Nathalie Conte > Sent: Monday, May 16, 2011 10:14 AM > To: Bioconductor mailing list > Subject: [BioC] [Fwd: help in annotation ILLUMINA probes] > > Dear all, > I have a set of probes Ids from illumina beads arrays > > illuminaProbeID > ILMN_1250814 > ILMN_1257855 > ILMN_2537948 > ILMN_3144164 > ILMN_2636200 > > > what is the best way to fetch the chromosomal location of those ( chr: > start :end)? > > Many thanks > Nathalie > > > -- > ?The Wellcome Trust Sanger Institute is operated by Genome Research > ?Limited, a charity registered in England with number 1021457 and a > ?company registered in England with number 2742969, whose registered > ?office is 215 Euston Road, London, NW1 2BE. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > IMPORTANT WARNING: ?This email (and any attachments) is ...{{dropped:9}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Tue, 17 May 2011 17:12:13 +0900, Mark Dunning <mark.dunning at="" gmail.com=""> wrote: > Hi Nathalie, > > You can use the illumina Bioconductor annotation packages to do this. > The particular one you need is illuminaMousev2.db > >> library(illuminaMousev2.db) > >> ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164", >> "ILMN_2636200") > >> mget(ids, illuminaMousev2GENOMICLOCATION) Dear Mark, I ran the code but came across some problems. Here's my history library("AnnotationDbi") source("http://bioconductor.org/biocLite.R") biocLite("illuminaMousev2.db") library(illuminaMousev2.db) ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164", "ILMN_2636200") mget(ids, illuminaMousev2GENOMICLOCATION) Error: object 'illuminaMousev2GENOMICLOCATION' not found Error in mget(ids, illuminaMousev2GENOMICLOCATION) : error in evaluating the argument 'envir' in selecting a method for function 'mget' sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaMousev2.db_1.6.1 org.Mm.eg.db_2.4.1 RSQLite_0.9-2 [4] DBI_0.2-5 AnnotationDbi_1.10.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] tools_2.11.0 Cheers, -- Dave
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Hi Dave, On Wed, May 25, 2011 at 11:10 PM, Dave Tang <davetingpongtang at="" gmail.com=""> wrote: > On Tue, 17 May 2011 17:12:13 +0900, Mark Dunning <mark.dunning at="" gmail.com=""> > wrote: > >> Hi Nathalie, >> >> You can use the illumina Bioconductor annotation packages to do this. >> The particular one you need is illuminaMousev2.db >> >>> library(illuminaMousev2.db) >> >>> ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164", >>> "ILMN_2636200") >> >>> mget(ids, illuminaMousev2GENOMICLOCATION) > > Dear Mark, > > I ran the code but came across some problems. Here's my history > > library("AnnotationDbi") > source("http://bioconductor.org/biocLite.R") > biocLite("illuminaMousev2.db") > library(illuminaMousev2.db) > ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164", > "ILMN_2636200") > mget(ids, illuminaMousev2GENOMICLOCATION) > > Error: object 'illuminaMousev2GENOMICLOCATION' not found > Error in mget(ids, illuminaMousev2GENOMICLOCATION) : > ?error in evaluating the argument 'envir' in selecting a method for function > 'mget' > > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu As a general rule of thumb, you should be running the latest version of the R and bioconductor combo to get the most milage out of the help on this mailing list. The latest version of R is 2.13.0, which was recently released. If you use that with the appropriate bioconductor version (v 2.8 -- which is chosen automatically for you when installing via biocLite()) the code works as advertised. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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On Thu, 26 May 2011 12:30:33 +0900, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > As a general rule of thumb, you should be running the latest version > of the R and bioconductor combo to get the most milage out of the help > on this mailing list. > The latest version of R is 2.13.0, which was recently released. If you > use that with the appropriate bioconductor version (v 2.8 -- which is > chosen automatically for you when installing via biocLite()) the code > works as advertised. Hi Steve, Thank you for the reply and the kind note. I will make sure I'm up to date in the future. Cheers, -- Dave
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