Hi, PCA is also quite simple using ade4. install.package("ade4") library(ade4) data(rhone) dd1 <- dudi.pca(rhone$tab, nf = 4, scann = FALSE) scatter(dd1, sub = "Principal component analysis") For more examples: example(dudi.pca) # principal component analysis example(dudi.coa) # Correspondence analysis eg: fellenberg et al., 2001 Aedin Culhane On Wed, 2003-11-26 at 07:43, Natalie Thorne wrote: > PCA analysis is simple enough using prcomp function from the mva R > library. The help is quite good so you should be able to figure it out > from there. > > For 3D plots try the R library package xgobi...I've used it before and its > quite good. > > Natalie > > * * Natalie Thorne, Phd Student. > * * > * * Genetics and Bioinformatics Division, > * The Walter And Eliza Hall Institute > * * Of Medical Research (WEHI). > * * PO Royal Melbourne Hospital, 3050 > * * PH: +61 3 9345 2631 > * Fax: +61 3 9347 0852 > * * URL http://bioinf.wehi.edu.au > * * > * * Mathematics and Statistics Department, > * The University of Melbourne > * * Fax: +61 3 9344 4599 > * * > * * > * CRC for discovery of genes for common > * * human diseases. > * * > * * Email : thorne@wehi.edu.au > > On Wed, 26 Nov 2003, Anthony Bosco wrote: > > > Hi. > > > > I am interested in doing pca analysis on affymetrix data and ploting > > 3 components (in 3-D). > > > > Does anyone know how to do this? > > > > > > Regards > > > > > > Anthony > > > > -- > > ______________________________________________ > > > > Anthony Bosco - Cell Biology Research Assistant > > > > Institute for Child Health Research > > (Company Limited by Guarantee ACN 009 278 755) > > Subiaco, Western Australia, 6008 > > > > Ph 61 8 9489 , Fax 61 8 9489 7700 > > email anthonyb@ichr.uwa.edu.au > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Aedin Culhane Conway Institute University College Dublin Belfied, Dublin 4 Ireland Phone: +353 (0)1 7166834 Fax: +353 (0)1 7166701 Email: Aedin.Culhane@ucd.ie