Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconductor?
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Jinyan Huang ▴ 10
@jinyan-huang-4492
Last seen 8.4 years ago
Hi list, At this websites http://www.bioconductor.org/help/bioc-views/release/data/annotation/, I cannot find it. Thanks.
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@michal-okoniewski-2676
Last seen 8.4 years ago
Chances are that there is no such thing :) Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore. If you want gene level summaries - go for Brainarray CDFs. Cheers, Michal ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Jinyan Huang [huangjy.tongji@gmail.com] Sent: Thursday, February 17, 2011 12:05 PM To: mailman, bioconductor Subject: [BioC] Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconductor? Hi list, At this websites http://www.bioconductor.org/help/bioc-views/release/data/annotation/, I cannot find it. Thanks. _______________________________________________ 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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Hi Jinyan, So there is not presently a package for this. And is a little more complicated since this is an exon chip and the gene annotations are all gene-centric. But you could still generate an annotation package if you had a mapping between the exon probesets and some kind of universal gene identifier (like an entrez gene ID). If you have a mapping like this (probeset to gene) you could then easily generate a package by following the SQLForge instructions in AnnotationDbi here: http://www.bioconductor.org/help/bioc- views/release/bioc/html/AnnotationDbi.html Marc ----- Original Message ----- From: "Michal Okoniewski" <michal.okoniewski@fgcz.ethz.ch> To: "Jinyan Huang" <huangjy.tongji at="" gmail.com="">, "bioconductor mailman" <bioconductor at="" r-project.org=""> Sent: Thursday, February 17, 2011 3:32:06 AM Subject: Re: [BioC] Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconductor? Chances are that there is no such thing :) Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore. If you want gene level summaries - go for Brainarray CDFs. Cheers, Michal ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Jinyan Huang [huangjy.tongji@gmail.com] Sent: Thursday, February 17, 2011 12:05 PM To: mailman, bioconductor Subject: [BioC] Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconductor? Hi list, At this websites http://www.bioconductor.org/help/bioc-views/release/data/annotation/, I cannot find it. Thanks. _______________________________________________ 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 _______________________________________________ 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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It is also likely worth studying http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/doc /V5ExonGene.pdf which shows how NetAffx annotations can be collected and attached to exon chip representations. You can get a lot of mileage out of the pd.huex.st.1.0.v2 with oligo package for analyzing exon arrays On Fri, Feb 18, 2011 at 2:09 PM, Carlson, Marc R <mcarlson@fhcrc.org> wrote: > Hi Jinyan, > > So there is not presently a package for this. And is a little more > complicated since this is an exon chip and the gene annotations are all > gene-centric. But you could still generate an annotation package if you had > a mapping between the exon probesets and some kind of universal gene > identifier (like an entrez gene ID). If you have a mapping like this > (probeset to gene) you could then easily generate a package by following the > SQLForge instructions in AnnotationDbi here: > > > http://www.bioconductor.org/help/bioc- views/release/bioc/html/AnnotationDbi.html > > > Marc > > > > ----- Original Message ----- > From: "Michal Okoniewski" <michal.okoniewski@fgcz.ethz.ch> > To: "Jinyan Huang" <huangjy.tongji@gmail.com>, "bioconductor mailman" < > bioconductor@r-project.org> > Sent: Thursday, February 17, 2011 3:32:06 AM > Subject: Re: [BioC] Is there annotation package for Affymetrix Human Exon > 1.0 ST Array on bioconductor? > > Chances are that there is no such thing :) > Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore. > If you want gene level summaries - go for Brainarray CDFs. > > Cheers, > Michal > ________________________________________ > From: bioconductor-bounces@r-project.org [ > bioconductor-bounces@r-project.org] on behalf of Jinyan Huang [ > huangjy.tongji@gmail.com] > Sent: Thursday, February 17, 2011 12:05 PM > To: mailman, bioconductor > Subject: [BioC] Is there annotation package for Affymetrix Human Exon 1.0 > ST Array on bioconductor? > > Hi list, > > At this websites > http://www.bioconductor.org/help/bioc- views/release/data/annotation/, > I cannot find it. > > Thanks. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Marc, Thanks for your suggestion. It is clear for this. On Fri, Feb 18, 2011 at 8:29 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > It is also likely worth studying > > http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/d oc/V5ExonGene.pdf > > which shows how NetAffx annotations can be collected and attached to exon > chip representations. ?You can get a lot of mileage out of the > pd.huex.st.1.0.v2 with oligo package for analyzing exon arrays > > On Fri, Feb 18, 2011 at 2:09 PM, Carlson, Marc R <mcarlson at="" fhcrc.org=""> wrote: > >> Hi Jinyan, >> >> So there is not presently a package for this. ?And is a little more >> complicated since this is an exon chip and the gene annotations are all >> gene-centric. ?But you could still generate an annotation package if you had >> a mapping between the exon probesets and some kind of universal gene >> identifier (like an entrez gene ID). ?If you have a mapping like this >> (probeset to gene) you could then easily generate a package by following the >> SQLForge instructions in AnnotationDbi here: >> >> >> http://www.bioconductor.org/help/bioc- views/release/bioc/html/AnnotationDbi.html >> >> >> ?Marc >> >> >> >> ----- Original Message ----- >> From: "Michal Okoniewski" <michal.okoniewski at="" fgcz.ethz.ch=""> >> To: "Jinyan Huang" <huangjy.tongji at="" gmail.com="">, "bioconductor mailman" < >> bioconductor at r-project.org> >> Sent: Thursday, February 17, 2011 3:32:06 AM >> Subject: Re: [BioC] Is there annotation package for Affymetrix Human Exon >> 1.0 ST ? ? ? ?Array on bioconductor? >> >> Chances are that there is no such thing :) >> Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore. >> If you want gene level summaries - go for Brainarray CDFs. >> >> Cheers, >> Michal >> ________________________________________ >> From: bioconductor-bounces at r-project.org [ >> bioconductor-bounces at r-project.org] on behalf of Jinyan Huang [ >> huangjy.tongji at gmail.com] >> Sent: Thursday, February 17, 2011 12:05 PM >> To: mailman, bioconductor >> Subject: [BioC] Is there annotation package for Affymetrix Human Exon 1.0 >> ST ? ?Array on bioconductor? >> >> Hi list, >> >> At this websites >> http://www.bioconductor.org/help/bioc- views/release/data/annotation/, >> I cannot find it. >> >> Thanks. >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> 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 >> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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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