ENTREZ identifiers for PGSEA
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@sebastien-gerega-2229
Last seen 8.1 years ago
Hi, I would like to use a lumi expression set with the PGSEA package and GO to generate genesets. I understand that the identifiers used in the data matrix need to be the same as those used in the genesets. Therefore, since I am using the GO database I need to use the ENTREZ identifiers for my matrix. How can I go about doing this? Obviously I cannot have multiple rows with the same name so I will have to remove duplicates and should probably do so based on variance or something. Is there an elegant way to do what I need? thanks, Sebastien
GO lumi PGSEA GO lumi PGSEA • 934 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
You could use the findLargest() function in Biobase to select identifers that have the largest differences between your samples. Best, Jim Sebastien Gerega wrote: > Hi, > I would like to use a lumi expression set with the PGSEA package and GO > to generate genesets. I understand that the identifiers used in the data > matrix need to be the same as those used in the genesets. Therefore, > since I am using the GO database I need to use the ENTREZ identifiers > for my matrix. How can I go about doing this? Obviously I cannot have > multiple rows with the same name so I will have to remove duplicates and > should probably do so based on variance or something. Is there an > elegant way to do what I need? > thanks, > Sebastien > > _______________________________________________ > 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 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Dykema, Karl ▴ 90
@dykema-karl-1116
Last seen 8.1 years ago
Hi all, We have been having an offline discussion of this issue. I am posting the correspondence so that it can be referenced in the future. Thanks. -karl Sebastien, Nope, you are doing it exactly right. I fixed that problem a while ago but apparently neglected to upload my code changes to Bioconductor... In the mean time here is the fixed function for you to use: aggregateExprs <- function(x,package="hgu133plus2",using="ENTREZID",FUN,...) { if(class(x) != "matrix" && !is(x, "ExpressionSet")) stop("need matrix or ExpressionSet") if(is.null(package) && is(x, "ExpressionSet")) package <- annotation(x) if(is.null(package)) stop("annotation package name is required") if(!require(package,character.only=TRUE)) stop(package," is not available") pPos <- paste("package",package,sep=":") if(grep(".*db",package)) package <- gsub(".db","",package) nEnv <- paste(package,using,sep="") Env <- get(nEnv,pos=pPos) if(is(x, "ExpressionSet")) { ids <- featureNames(x) x <- exprs(x) } else { ids <- rownames(x) } lls <- mget(ids,env=Env,ifnotfound=NA) if(length(lls)!=length(unlist(lls))) for(i in 1:length(lls)) lls[[i]] <- lls[[i]][1] lls <- unlist(lls) f <- factor(lls) undupx <- aggregate(x,by=list(f),FUN,...) rownames(undupx) <- as.character(undupx[,1]) undupx <- as.matrix(undupx[,-1]) return(undupx) } -karl -----Original Message----- From: Sebastien Gerega [mailto:sgerega@gmail.com] On Behalf Of Sebastien Gerega Sent: Wednesday, July 09, 2008 7:17 PM To: Dykema, Karl Subject: Re: [BioC] ENTREZ identifiers for PGSEA Hi, thanks for your reply. I have just had a quick go using the following command: aggregateExprs(exprs(eset), "lumiHumanAll", FUN=mean, na.rm=TRUE) but I get the error: "There is no package called "lumiHumanAll" If I try specifying the library as "lumiHumanAll.db" then I get the error: variable "lumiHumanAll.dbENTREZID" was not found... Am I doing something wrong? thanks, Sebastien Dykema, Karl wrote: > Sebastien, > > You should take a look at our function "aggregateExprs". As long as you have an annotation environment for your lumi microarray, it is quite simple. Let me know if you run into any problems. > > -karl > > > > ------ Forwarded Message > From: Sebastien Gerega <seb at="" gerega.net=""> > Date: Wed, 09 Jul 2008 16:31:29 +1000 > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] ENTREZ identifiers for PGSEA > > Hi, > I would like to use a lumi expression set with the PGSEA package and GO > to generate genesets. I understand that the identifiers used in the data > matrix need to be the same as those used in the genesets. Therefore, > since I am using the GO database I need to use the ENTREZ identifiers > for my matrix. How can I go about doing this? Obviously I cannot have > multiple rows with the same name so I will have to remove duplicates and > should probably do so based on variance or something. Is there an > elegant way to do what I need? > thanks, > Sebastien > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor This email message, including any attachments, is for th...{{dropped:6}}
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