Hi Marco, That sounds reasonable. I will add this functionality to the devel version of affycoretools, probably this week. You don't mention your OS, but if you are on Windows I might need to send you a binary, as the binary affycoretools tends not to get built until close to release time (because it depends on biomaRt, which depends on RCurl, which takes a bit of work to build on windows...). Best, Jim marco fabbri wrote: > Hi James, > thank you for the quick reply. > More than plot all the three PCs, I would like to decide which two to > plot, for example to plot PC2 versus PC3. > If you are implementing please let me know I will use for sure. > > Marco > > On 14/11/06, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > >> Hi Marco, >> >> marco fabbri 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? >> >> No you are not wrong. By default plotPCA() only does the first two >> principal components. If there is interest I could easily add the >> capability to do the first three PCs and plot using scatterplot3D. >> >> > >> > 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? >> >> plotPCA() is using the default arguments to prcomp(), which includes >> scale.=FALSE. Usually one wants to scale data prior to performing the >> PCA if the data are on different scales. However, most Affy data are >> normalized which should put the data on similar scales, so I just stick >> with the default. >> >> >> HTH, >> >> Jim >> >> >> > >> > >> > Thank you >> > MArco >> > >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues. >> > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.