Getting all the gene names and the locus link ID from different platforms
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Alex Tsoi ▴ 260
@alex-tsoi-2154
Last seen 9.6 years ago
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
Alex Tsoi wrote: > Dear all, > > I am trying to get ALL the gene names (symbol) and their corresponding locus > link ID from around 10 different Affymetrix platforms, but I am not quite > sure how to do that.....effeciently. > > I know I could use the aafSymbol from the annaffy package or the getLL / > getSYMBOL from the annotate package to do that, but all of these functions > require to input a set of identifiers (the probesets), and in my case, I > will have to get ALL the probesets from my experiment first, and then call > the function to get all the Locus Link id / symbol corresponding to that > chip. > > Do you guys have some more effecient ways to retrieve all the locus link id > or the symbol from different affymetrix platforms ? I greatly appreciate for > the help. > > Thanks a lot, > > You could use the LL Mappings packages. The only catch is that then you will have all the entrez gene IDs which would go well beyond your current ten platforms. We don't have a list of all the probesets from your ten platforms, so we can only meet you halfway on this. ;) Marc
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
> >I am trying to get ALL the gene names (symbol) and their corresponding locus >link ID from around 10 different Affymetrix platforms, but I am not quite >sure how to do that.....effeciently. > >I know I could use the aafSymbol from the annaffy package or the getLL / >getSYMBOL from the annotate package to do that, but all of these functions >require to input a set of identifiers (the probesets), and in my case, I >will have to get ALL the probesets from my experiment first, and then call >the function to get all the Locus Link id / symbol corresponding to that >chip. > >Do you guys have some more effecient ways to retrieve all the locus link id >or the symbol from different affymetrix platforms ? I greatly appreciate for >the help. Is this what you want? >lilbrary(hgu95av2) >geneNames <- mget(ls(hgu95av2SYMBOL), hgu95av2SYMBOL) > >Thanks a lot, > >-- >Lam C. Tsoi (Alex) >Medical University of South Carolina > > [[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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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