[BioC] RefPlus error

[Harbron, Chris]

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 at 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



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