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 P?rez 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 P?rez 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]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor