list of annaffy .db files?
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@andrew-einhorn-4221
Last seen 8.1 years ago
I am trying to use annaffy to annotate a hugene10stv1 array. I cannot find the name of the .db annotation packages I am supposed to install. My code thus far looks like: anncols <- aaf.handler()[c(1:4, 6,11)] anntable <- aafTableAnn(rownames(exprs(results))[1:50], "insert package name", anncols) Is there a list somewhere of the names of all the annaffy .db files? Regards Andrew [[alternative HTML version deleted]]
Annotation annotate annaffy Annotation annotate annaffy • 715 views
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@vincent-j-carey-jr-4
Last seen 20 days ago
United States
there are no annaffy .db files -- the .db annotation paradigm is independent of annaffy see the annotationDbi vignette for more background for the ST array you can probably work from the package at http://www.bioconductor.org/packages/release/data/annotation/html/huge ne10sttranscriptcluster.db.html but there is also a probeset version On Tue, Aug 31, 2010 at 10:46 AM, Andrew Einhorn <andreweinhorn at="" gmail.com=""> wrote: > I am trying to use annaffy to annotate a hugene10stv1 array. ?I cannot find > the name of the .db annotation packages I am supposed to install. ?My code > thus far looks like: > > anncols <- aaf.handler()[c(1:4, 6,11)] > anntable <- aafTableAnn(rownames(exprs(results))[1:50], "insert package > name", anncols) > > Is there a list somewhere of the names of all the annaffy .db files? > > Regards > > 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, In addition to Vince's helpful comments, you can find a list of the pre-made Bioconductor annotation packages here: http://www.bioconductor.org/packages/devel/data/annotation/ And if you need to make your own .db package, you can use the SQLForge vignette (which is also in the AnnotationDbi package). Marc On 08/31/2010 07:57 AM, Vincent Carey wrote: > there are no annaffy .db files -- the .db annotation paradigm is > independent of annaffy > > see the annotationDbi vignette for more background > > for the ST array you can probably work from the package at > > http://www.bioconductor.org/packages/release/data/annotation/html/hu gene10sttranscriptcluster.db.html > > but there is also a probeset version > > On Tue, Aug 31, 2010 at 10:46 AM, Andrew Einhorn > <andreweinhorn at="" gmail.com=""> wrote: > >> I am trying to use annaffy to annotate a hugene10stv1 array. I cannot find >> the name of the .db annotation packages I am supposed to install. My code >> thus far looks like: >> >> anncols <- aaf.handler()[c(1:4, 6,11)] >> anntable <- aafTableAnn(rownames(exprs(results))[1:50], "insert package >> name", anncols) >> >> Is there a list somewhere of the names of all the annaffy .db files? >> >> Regards >> >> 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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