[BioC] Problems in MAplot for affybatch objects

[Ben Bolstad]

Hi Javier,

You have indeed found discrepant behavior that should be fixed. MAplot
for ExpressionSet object is implemented in affyPLM, MAplot for AffyBatch
objects is implemented in affy. So it is not really the same set of code
being executed in each case. But the basic behavior was intended to be
harmonious between the two. I will fix.

Ben




On Sat, 2010-04-10 at 16:47 +0200, Javier Pérez Florido wrote:
> 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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