[BioC] ENTREZ identifiers for PGSEA

[Dykema, Karl]

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 at 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


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