how often are annotation packages updated (with respect to hgu133a.db and hgu133plus2.db)
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
Hi, a naive question that relates to the annotation data packages: how often are they updated? Take for example hgu133a.db and hgu133plus2.db. I'm using versions 2.2.11 for both of them. With the hgu133plus2.db, mget('206902_s_at', env=hgu133plus2ENTREZID) returns 9941 as the Entrez ID However, mget('206902_s_at', env=hgu133aENTREZID) returns NA, whereas on the Affymetrix website, the probe set id returns 9941 as the Entrez ID Does this imply that the hgu133a.db package is out of date? Thanks, Andrew [[alternative HTML version deleted]]
Annotation hgu133a hgu133plus2 probe Annotation hgu133a hgu133plus2 probe • 807 views
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@kasper-daniel-hansen-2979
Last seen 5 months ago
United States
As has been discussed multiple times on the list, essentially an annotation package is update bi-annually, in context with each Bioconductor release. Let us say the release dat is April 1st. Sometime before April 1st (probably within a few months of this date), someone (right now I believe it is Marc Carlson) will generate the annotation packages for the most recent version of the annotation available at that date. So first of all you need to make sure you are using the newest version of R. If that is not good enough, you will need to build it from scratch yourself. I would be surprised if you find many discrepancies, given that Bioconductor was released very recently. But I am also not up to date on Affy's release cycle for their annotation. KAsper On May 6, 2009, at 15:00 , Andrew Yee wrote: > Hi, a naive question that relates to the annotation data packages: > how > often are they updated? > > Take for example hgu133a.db and hgu133plus2.db. I'm using versions > 2.2.11 > for both of them. > > With the hgu133plus2.db, > > mget('206902_s_at', env=hgu133plus2ENTREZID) > > returns 9941 as the Entrez ID > > However, > > mget('206902_s_at', env=hgu133aENTREZID) > > returns NA, whereas on the Affymetrix website, the probe set id > returns 9941 > as the Entrez ID > > Does this imply that the hgu133a.db package is out of date? > > Thanks, > Andrew > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks for the reply. I'm actually using R 2.9. Andrew On Wednesday, May 6, 2009, Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> wrote: > As has been discussed multiple times on the list, essentially an annotation package is update bi-annually, in context with each Bioconductor release. > > Let us say the release dat is April 1st. Sometime before April 1st (probably within a few months of this date), someone (right now I believe it is Marc Carlson) will generate the annotation packages for the most recent version of the annotation available at that date. > > So first of all you need to make sure you are using the newest version of R. If that is not good enough, you will need to build it from scratch yourself. > > I would be surprised if you find many discrepancies, given that Bioconductor was released very recently. But I am also not up to date on Affy's release cycle for their annotation. > > KAsper > > > On May 6, 2009, at 15:00 , Andrew Yee wrote: > > > Hi, a naive question that relates to the annotation data packages: ?how > often are they updated? > > Take for example hgu133a.db and hgu133plus2.db. ?I'm using versions 2.2.11 > for both of them. > > With the hgu133plus2.db, > > mget('206902_s_at', env=hgu133plus2ENTREZID) > > returns 9941 as the Entrez ID > > However, > > mget('206902_s_at', env=hgu133aENTREZID) > > returns NA, whereas on the Affymetrix website, the probe set id returns 9941 > as the Entrez ID > > Does this imply that the hgu133a.db package is out of date? > > Thanks, > Andrew > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >
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Hi Andrew, The annotation packages are all updated every 6 months and hgu133a.db is no exception. However, after looking at this very closely I have decided to rebuild hgu133a.db. A new version of this package will be online very shortly and will only be slightly different. But the small issue you discovered will be gone. Marc Andrew Yee wrote: > Thanks for the reply. I'm actually using R 2.9. > > Andrew > > On Wednesday, May 6, 2009, Kasper Daniel Hansen > <khansen at="" stat.berkeley.edu=""> wrote: > >> As has been discussed multiple times on the list, essentially an annotation package is update bi-annually, in context with each Bioconductor release. >> >> Let us say the release dat is April 1st. Sometime before April 1st (probably within a few months of this date), someone (right now I believe it is Marc Carlson) will generate the annotation packages for the most recent version of the annotation available at that date. >> >> So first of all you need to make sure you are using the newest version of R. If that is not good enough, you will need to build it from scratch yourself. >> >> I would be surprised if you find many discrepancies, given that Bioconductor was released very recently. But I am also not up to date on Affy's release cycle for their annotation. >> >> KAsper >> >> >> On May 6, 2009, at 15:00 , Andrew Yee wrote: >> >> >> Hi, a naive question that relates to the annotation data packages: how >> often are they updated? >> >> Take for example hgu133a.db and hgu133plus2.db. I'm using versions 2.2.11 >> for both of them. >> >> With the hgu133plus2.db, >> >> mget('206902_s_at', env=hgu133plus2ENTREZID) >> >> returns 9941 as the Entrez ID >> >> However, >> >> mget('206902_s_at', env=hgu133aENTREZID) >> >> returns NA, whereas on the Affymetrix website, the probe set id returns 9941 >> as the Entrez ID >> >> Does this imply that the hgu133a.db package is out of date? >> >> Thanks, >> Andrew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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