Question: list of annaffy .db files?
0
gravatar for Andrew Einhorn
9.1 years ago by
Andrew Einhorn80 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]]
annotation annotate annaffy • 484 views
ADD COMMENTlink modified 9.1 years ago by Vincent J. Carey, Jr.6.3k • written 9.1 years ago by Andrew Einhorn80
Answer: list of annaffy .db files?
0
gravatar for Vincent J. Carey, Jr.
9.1 years ago by
United States
Vincent J. Carey, Jr.6.3k 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/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 >
ADD COMMENTlink written 9.1 years ago by Vincent J. Carey, Jr.6.3k
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 >
ADD REPLYlink written 9.1 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 191 users visited in the last hour