I have a question about principal component analysis on microarray data. I found two functions for doing PCA, princomp and prcomp. The calculation in prcomp is done by a singular value decomposition which is not what I want to do. The problem with princomp is that the function seems to scale the data by default. Since I am dealing with log rations there is no reason to scale the data because it is on a comparable scale. Is there some way of doing PCA in R on microarray data without having to scale the data? Best regards // Johan Lindberg [[alternative HTML version deleted]]

Dear Johan, On Thursday 11 November 2004 17:01, Johan Lindberg wrote: > I have a question about principal component analysis on microarray data. > > I found two functions for doing PCA, princomp and prcomp. > > The calculation in prcomp is done by a singular value decomposition > which is not what I want to do. Why? prcomp uses svd because of numerical stability issues, and using svd is a standard way of doing PCA. The help for princomp says: " The calculation is done using 'eigen' on the correlation or covariance matrix, as determined by 'cor'. This is done for compatibility with the S-PLUS result. A preferred method of calculation is to use 'svd' on 'x', as is done in 'prcomp'." > > The problem with princomp is that the function seems to scale the data > by default. Since I am dealing with log rations there is no reason to > scale the data because it is on a comparable scale. Is there some way of > doing PCA in R on microarray data without having to scale the data? if you do ?prcomp you'll see you can set the "scale." argument to FALSE. Best, R. > > Best regards > > // Johan Lindberg > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc)