[BioC] PCA-prcomp() versus plotPCA

[marco fabbri]

Two question on PCA:

1. I like plotPCA from affycoretools package, but I was not able to
plot the third component.
Am I wrong?

2.I try the prcomp() function and  I compared it to plotPCA.

TesetA=t(exprs(esetA))
pca=prcomp(TAM,  retx=TRUE,center=TRUE, scale= TRUE)
plot(pca$x[,1:2])
--------
plotPCA(esetA,groups=c(1:10))

I had different plots.
Can please help me to understand better what  plotPCA is doing?


Thank you
MArco

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Marco Fabbri
Istituto Clinico Humanitas
via Manzoni, 52
20089 Rozzano (Mi)
Tel. 028224 5152
Fax 028224 5101