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Question: getSYMBOL( ) error
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gravatar for Rao,Xiayu
4.4 years ago by
Rao,Xiayu530
United States
Rao,Xiayu530 wrote:
Hello, I tried to find gene names that match affyIDs, and I tried two ways as below, but neither worked. I got all NAs for the Symbol column. I have no idea what happened. Thank you very much for helping me out! (1) library(affy) mydata <- ReadAffy() eset <- rma(mydata) library(annotate) library(hgu95av2.db) ID <- featureNames(eset) Symbol <- getSYMBOL(ID,"hgu95av2.db") fData(eset) <- data.frame(ID=ID,Symbol=Symbol) All NAs for Symbol in the topTable (2) fit$genes$Symbol <- getSYMBOL(fit$genes$ID, "hgu95av2.db") >fit $genes ID Symbol 1 7892501 NA 2 7892502 NA 3 7892503 NA 4 7892504 NA 5 7892505 NA 32316 more rows ... Thanks, Xiayu [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.4 years ago by James W. MacDonald45k • written 4.4 years ago by Rao,Xiayu530
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gravatar for James W. MacDonald
4.4 years ago by
United States
James W. MacDonald45k wrote:
Hi Xaiyu, On 7/8/2013 6:13 PM, Rao,Xiayu wrote: > Hello, > > I tried to find gene names that match affyIDs, and I tried two ways as below, but neither worked. I got all NAs for the Symbol column. I have no idea what happened. Thank you very much for helping me out! > > (1) library(affy) > mydata<- ReadAffy() > eset<- rma(mydata) > library(annotate) > library(hgu95av2.db) > ID<- featureNames(eset) > Symbol<- getSYMBOL(ID,"hgu95av2.db") > fData(eset)<- data.frame(ID=ID,Symbol=Symbol) > > All NAs for Symbol in the topTable > > (2) fit$genes$Symbol<- getSYMBOL(fit$genes$ID, "hgu95av2.db") > >> fit > $genes > ID Symbol > 1 7892501 NA > 2 7892502 NA > 3 7892503 NA > 4 7892504 NA > 5 7892505 NA > 32316 more rows ... Those aren't hgu95av2 probe IDs. They appear to be hugene 1.0 transcript cluster IDs. So you need to use the hugene10sttranscriptcluster.db package. Best, Jim > > Thanks, > Xiayu > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.4 years ago by James W. MacDonald45k
Oh, I see. Thank you very much for your kind help, James! -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Tuesday, July 09, 2013 11:19 AM To: Rao,Xiayu Cc: 'bioconductor at r-project.org' Subject: Re: [BioC] getSYMBOL( ) error Hi Xaiyu, On 7/8/2013 6:13 PM, Rao,Xiayu wrote: > Hello, > > I tried to find gene names that match affyIDs, and I tried two ways as below, but neither worked. I got all NAs for the Symbol column. I have no idea what happened. Thank you very much for helping me out! > > (1) library(affy) > mydata<- ReadAffy() > eset<- rma(mydata) > library(annotate) > library(hgu95av2.db) > ID<- featureNames(eset) > Symbol<- getSYMBOL(ID,"hgu95av2.db") > fData(eset)<- data.frame(ID=ID,Symbol=Symbol) > > All NAs for Symbol in the topTable > > (2) fit$genes$Symbol<- getSYMBOL(fit$genes$ID, "hgu95av2.db") > >> fit > $genes > ID Symbol > 1 7892501 NA > 2 7892502 NA > 3 7892503 NA > 4 7892504 NA > 5 7892505 NA > 32316 more rows ... Those aren't hgu95av2 probe IDs. They appear to be hugene 1.0 transcript cluster IDs. So you need to use the hugene10sttranscriptcluster.db package. Best, Jim > > Thanks, > Xiayu > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 4.4 years ago by Rao,Xiayu530
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