[BioC] Error when running expresso

[Rafael A. Irizarry]

this is probably because your data set has only one array. notice,
quantile normalization doesnt mean much when you just have one array it 
is equivalent to not normalizing. however, you shouldnt get an error.

source this in, while we fix the bug:
normalize.AffyBatch.quantiles <- function (abatch, pmonly = FALSE){
  pms <- unlist(pmindex(abatch))
  noNA <- apply(intensity(abatch)[pms,,drop=FALSE ], 1, function(x)
                all(!is.na(x)))
  pms <- pms[noNA]
  intensity(abatch)[pms,] <-
    normalize.quantiles(intensity(abatch)[pms,,drop=FALSE])
  if (!pmonly) {
    mms <- unlist(mmindex(abatch))
    noNA <- apply(intensity(abatch)[mms, ,drop=FALSE], 1, function(x)
                  all(!is.na(x)))
    mms <- mms[noNA]
    intensity(abatch)[mms,]<-
      normalize.quantiles(intensity(abatch)[mms,,drop=FALSE])
  }
  return(abatch)
}

On Fri, 20 Jun 2003, Kelvin Yen wrote:  

> I recently installed R 1.7.1 and tried analyzing my data by running 
> rma via expresso and get the following error:
> 
> >  expresso(data,widget=TRUE)
> background correction: rma
> normalization: quantiles
> PM/MM correction : pmonly
> expression values: medianpolish
> background correcting...done.
> normalizing...Error in apply(intensity(abatch)[pms, ], 1, function(x) 
> all(!is.na(x))) :
>          dim(X) must have a positive length
> 
> If I run "rma(data)" I don't get the error and when I ran the above 
> on R 1.6.1 I didn't get an error.  Anyone have an idea as to why I 
> get the error?  The reason why I want to run rma via expresso is so I 
> can use the MAS summary method.
> 
> Kelvin
> 
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