Question: PCA-prcomp() versus plotPCA

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marco fabbri •

**320**wrote: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

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modified 13.1 years ago
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James W. MacDonald ♦

**52k**• written 13.1 years ago by marco fabbri •**320**