[BioC] Situation of the legend in the plotPCA of the affycoretools library

[Jordi Altirriba Gutiérrez]

Dear BioC users,
I am trying to do a PCA plot with the package affycoretools, which I have 
found very useful!
I am not able to change the situation of the legend in the plot, although I 
have introduced the variables x.coord and y.coord in the script. Could it be 
a little bug or am I doing something wrong?
Many thanks in advance!

This is my code:
library(affycoretools)
Data<-ReadAffy()
eset<-rma(Data)
pd <- read.phenoData("pdata2.txt", header = TRUE, row.names = 1)
plotPCA(eset,groups = rep(1:2, each = 3), groupnames = 
unique(pData(pd))[,1],addtext=sampleNames(Data))

I obtain exactly the same plot writing:
plotPCA(eset,groups = rep(1:2, each = 3), groupnames = 
unique(pData(pd))[,1],addtext=sampleNames(Data),x.coord=0,y.coord=0)

My session:
>sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
   rat2302cdf affycoretools       GOstats      Category      hgu95av2
     "1.12.0"       "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"
         KEGG      multtest    genefilter      survival        xtable
     "1.12.0"      "1.10.2"      "1.10.1"        "2.28"       "1.3-2"
         RBGL      annotate            GO         graph         Ruuid
      "1.8.1"      "1.10.0"      "1.12.0"      "1.10.6"      "1.10.0"
        limma          affy        affyio       Biobase
     "2.7.10"      "1.10.0"       "1.0.0"      "1.10.1"

Jordi Altirriba
PhD student
Hospital Clinic (Barcelona, Spain)