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Have a look at the standard R packages prcomp and princomp they do the same thing but differently. regards, Arne -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Yanqin Yang Sent: Tuesday, July 12, 2005 19:52 To: bioconductor at stat.math.ethz.ch Subject: [BioC] PCA Hi everyone, I have 13 agilent human 44k chips. Would anyone tell me which bioconductor package or function could run principal component analysis? Thanks! Yanqin __________________________________________________ [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Dear Yanqin For PCA of microarary data, have a look at ord funtion in the bioconductor package made4. It simplified running PCA (and correspondence analysis) on microarray data. It takes input data in many formats including AffyBatch, ExprSet, data.frame etc. To run a PCA pca.res<- ord(data, "pca") plot(pca.res) Regards Aedin