Question: convert gene name to Affy ID
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6.9 years ago by
Guest User12k
Guest User12k wrote:
I've done plenty of preprocessing, just for the sake of statistical methods, but right now I find myself being rather illiterate when it comes to finding out about specific genes. I gather I have to use something like get(<myfavoritegene_name>, revmap(<description_of_array>)) but unfortunately I'm blanking on the details. It would be great to get some help. Specifically, what to use to describe the array I'm using In this instance, I need this for both the old and the new version of Affy's drosophila gene expression array, but if you could just point me into the direction where to find those names for whichever chip and any associated libraries or files I need. Many thanks for any clues. Julia -- output of sessionInfo(): get(<myfavoritegene_name>, revmap(<description_of_array>)) -- Sent via the guest posting facility at bioconductor.org.
preprocessing • 1.5k views
ADD COMMENTlink modified 6.9 years ago by Julia Brettschneider10 • written 6.9 years ago by Guest User12k
Answer: convert gene name to Affy ID
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gravatar for Marc Carlson
6.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Julia, I have written a vignette specifically for folks like you who are getting started using annotations. You can find it here: www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationDbi/inst/d oc/IntroToAnnotationPackages.pdf Hope this helps, Marc On 12/11/2012 02:06 PM, Julia Brettschneider [guest] wrote: > I've done plenty of preprocessing, just for the sake of statistical methods, but right now I find myself being rather illiterate when it comes to finding out about specific genes. > > I gather I have to use something like > get(<myfavoritegene_name>, revmap(<description_of_array>)) > but unfortunately I'm blanking on the details. > It would be great to get some help. > > Specifically, what to use to describe the array I'm using > In this instance, I need this for both the old and the new version of Affy's drosophila gene expression array, but if you could just point me into the direction where to find those names for whichever chip and any associated libraries or files I need. > > Many thanks for any clues. > Julia > > > -- output of sessionInfo(): > > get(<myfavoritegene_name>, revmap(<description_of_array>)) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
ADD COMMENTlink written 6.9 years ago by Marc Carlson7.2k
Answer: convert gene name to Affy ID
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gravatar for Julia Brettschneider
6.9 years ago by
Julia Brettschneider10 wrote:
Hi Marc, that looks terrific indeed! I'm looking the details right now to figure out whether that all applies to drosophila or is just for human. Many thanks, Julia
ADD COMMENTlink written 6.9 years ago by Julia Brettschneider10
Hi Julia, if you check the list of annotation packages already made in the Bioconductor page http://www.bioconductor.org/packages/release/BiocViews.html#___Annotat ionData you may find your array there. I don't know if this will be your array, but just for illustration purposes, I see that the array "Affymetrix Drosophila Genome 2.0 Array annotation data (chip drosophila2)" corresponds to the package 'drosophila2.db' If you download and install that, and look at the user guide for that package: http://www.bioconductor.org/packages/2.11/data/annotation/manuals/dros ophila2.db/man/drosophila2.db.pdf you should be able quite easily to match affymetrix ids to gene names, locations, and many other things. I hope this helps a bit. I have been lucky that all the arrays I have used were already annotated into a package :) Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
ADD REPLYlink written 6.9 years ago by J.delasHeras@ed.ac.uk1.9k
And if it's not there, you can try to follow the instructions in this vignette from the AnnotationForge package to generate an appropriate chip package: www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationForge/inst /doc/SQLForge.pdf Marc On 12/13/2012 03:46 AM, J.delasHeras at ed.ac.uk wrote: > Hi Julia, > > if you check the list of annotation packages already made in the > Bioconductor page > > http://www.bioconductor.org/packages/release/BiocViews.html#___Annot ationData > > > you may find your array there. > > I don't know if this will be your array, but just for illustration > purposes, I see that the array "Affymetrix Drosophila Genome 2.0 Array > annotation data (chip drosophila2)" corresponds to the package > 'drosophila2.db' > If you download and install that, and look at the user guide for that > package: > > http://www.bioconductor.org/packages/2.11/data/annotation/manuals/dr osophila2.db/man/drosophila2.db.pdf > > > you should be able quite easily to match affymetrix ids to gene names, > locations, and many other things. > > I hope this helps a bit. > I have been lucky that all the arrays I have used were already > annotated into a package :) > > Jose > > > > > > > >
ADD REPLYlink written 6.9 years ago by Marc Carlson7.2k
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