[BioC] Problems in MAplot for affybatch objects

[Ben Bolstad]

It has been fixed in affy 1.26.1/1.27.1 (Release/Devel) which will show
up in the builds sometime in the next few days.

Ben


On Wed, 2010-04-28 at 10:49 +0200, Javier Pérez Florido wrote:
> Dear Ben,
> I've installed the new version of both R and affyPLM package (1.24), but 
> the problem is still there....
> Thanks,
> Javier
> 
> 
> On 10/04/2010 21:51, Ben Bolstad wrote:
> > 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
> >>
> >>
> >> 	[[alternative HTML version deleted]]
> >>
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> >>      
> >
> >
> >
> 
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