That works well. Thanks. I am happy to stick with that, but I still do not understand why I get the error message "Error in svd(x, nu = 0) : infinite or missing values in 'x'", because looking at prcomp it should omit those genes that contain NA values when na.action=na.omit. I am interested in sample PCR, so there should be plenty of information left to do this. Any ideas? Dan Wolfram Stacklies wrote: > Hi Daniel, > > I am the maintainer of the pcaMethods package. The package provides several > PCA implementations that can handle missing data, so this should solve your > problem. Maybe you want to have a look at the ppca (probabilistic pca), > from > my experience it produces nice results. > You should take care about the amount of missing data, or or rows / > columns that > contain large numbers of missing values. For these the estimation may not be > very accurate (as there is little information to base the estimate on). > Better remove > them first... > If there are further questions I will be happy to answer them. > There will be a new release of the package coming with the new Bioconductor > release. This version contains many improvements, maybe you want to have > a look. > > Regards, > Wolfram > > > On 4/10/07, *Daniel Brewer* <daniel.brewer at="" icr.ac.uk=""> <mailto:daniel.brewer at="" icr.ac.uk="">> wrote: > > I have an expression matrix that contains NA values. What is the best > way to get: > 1) prcomp() (Exits with "Error in svd(x, nu = 0) : infinite or missing > values in 'x'") > 2) cor() (Exits with "Error in cor(exprs(Sperger)) : missing > observations in cov/cor") > to work with this type of matrix. > > Many Thanks > > Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}