RefPlus error
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@christian-ruckert-3294
Last seen 2.5 years ago
Germany
When using the rmaplus function from RefPlus package with only one sample in the AffyBatch object I get the following error message: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent The problem lies somewhere in function rmaref.predict, in the line: colnames(future)<-sampleNames(Future) where future has its dimensions switched. "rmaref.predict" <- function(Future,p.e){ ## Derive RMA+ expression. PMindex<-pmindex(Future) PM<-log2(pm(Future)) PM<-sweep(PM,1,unlist(p.e)) pm(Future)<-PM PMlist<-lapply(PMindex,function(x,y) intensity(y)[x,],Future) future<-t(sapply(PMlist,colMedians)) colnames(future)<-sampleNames(Future) return(future) } Greetings, Christian
RefPlus RefPlus • 673 views
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@harbron-chris-1976
Last seen 7.2 years ago
Dear Christian, Thanks for pointing this out. This is an example of R being over- efficient in its simplification of data structures from matrices down to vectors. We'll sort this out. In the short term can I suggest one of two workarounds: Either: Artificially create a duplicate sample in the AffyBatch, so that RefPlus thinks its dealing with two samples and the matrix simplification problem doesn't arise: affybatch.copy <- affybatch.example sampleNames(affybatch.copy) <- "COPY" affybatch.duplicate <- merge.AffyBatch(affybatch.example , affybatch.copy) Results <- rmaplus(affybatch.duplicate , rmapara=Para , bg = TRUE)[,1] or edit the function rmaref.predict() to include an extra line, so that it reads: rmaref.predict <- function (Future, p.e) { PMindex <- pmindex(Future) PM <- log2(pm(Future)) PM <- sweep(PM, 1, unlist(p.e)) pm(Future) <- PM PMlist <- lapply(PMindex, function(x, y) intensity(y)[x, ], Future) future <- t(sapply(PMlist, colMedians)) if(nrow(future)==1) {future <- t(future)} colnames(future) <- sampleNames(Future) return(future) } All the best Chris Harbron, Technical Lead Statistician, Discovery Statistics, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG. Chris.Harbron at AstraZeneca.Com ------------------------------ Message: 14 Date: Thu, 19 Feb 2009 17:57:35 +0100 From: Christian Ruckert <cruckert@uni-muenster.de> Subject: [BioC] RefPlus error To: bioconductor at stat.math.ethz.ch, Kai-Ming.Chang at astrazeneca.com Message-ID: <499D8F7F.2030603 at uni-muenster.de> Content-Type: text/plain; charset=ISO-8859-15; format=flowed When using the rmaplus function from RefPlus package with only one sample in the AffyBatch object I get the following error message: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent The problem lies somewhere in function rmaref.predict, in the line: colnames(future)<-sampleNames(Future) where future has its dimensions switched. "rmaref.predict" <- function(Future,p.e){ ## Derive RMA+ expression. PMindex<-pmindex(Future) PM<-log2(pm(Future)) PM<-sweep(PM,1,unlist(p.e)) pm(Future)<-PM PMlist<-lapply(PMindex,function(x,y) intensity(y)[x,],Future) future<-t(sapply(PMlist,colMedians)) colnames(future)<-sampleNames(Future) return(future) } Greetings, Christian ---------------------------------------------------------------------- ---- AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:21}}
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