Dear list,
I am trying to use MAplot (affyPLM packages) using 2 arrays for the 
argument 'which' and the same arrays for the argument 'ref'.
So

/library(affyPLM)
library(affydata)
data(Dilution) # Dilution data set
par(mfrow=c(2,1),1)
MAplot(Dilution,which=c(1,3),ref=c(1,3),plot.method="smoothScatter") /

I got the following warnings

/Warning messages
1: In if (i != ref) { :
   the condition has length > 1 and only the first element will be used
2: In if (i != ref) { :
   the condition has length > 1 and only the first element will be used/

The reference mean array is not built and, thus, the MAplot is not correct
However, the same piece of code on an expression set object works:
/
eset<-threestep(Dilution)
par(mfrow=c(2,1),1)
MAplot(eset,which=c(1,3),ref=c(1,3),plot.method="smoothScatter")/

What's the problem on affybatch objects?
Thanks in advance,
Javier


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