Hi, aneData is numeric but aneData_imp is not. But I have been told that because of the changes in knn.impute I now have to use aneData_imput$data instead of aneData_imp. I have tried this and now I do not get an error message any more. Regards, Ingrid > Ingrid H.G. ??stensen wrote: >> Hi >> >> I am running a microarray analysis that I have run before (on the same >> data set) but now I get an error message because my matrix suddenly is >> no >> longer numeric. Does anybody know what happens and how do solve it? >> Below >> I have pasted the commands and error message. >> >> Ingrid >> >> memory.limit(1300) >> library(limma) >> library(impute) >> aneTab <- >> read.table(file="S100A4_anes.txt",sep="\t",header=T,na.strings="") >> colnames(aneTab) >> aneData <- aneTab[,3:14] > > Are all the values in andData numeric? What do you get from str(aneData)? > > If the values are not all numeric, when you coerce to a matrix > everything will be coerced to some common type (often character). For > instance, if there are factors and numeric values in your data.frame, > they will all get coerced to character, which may be what is happening. > > HTH, > > Jim > > >> aneData <- as.matrix(aneData) >> is.matrix(aneData) >> aneData_imp <- impute.knn(aneData) >> aneDI_prc <-prcomp(t(aneData_imp)) >> Error in colMeans(x, n, prod(dn), na.rm) : >> 'x' must be numeric >> >> >> > > > -- > 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. > -- Ingrid H.G. ?stensen Bioinformatics user support (NMC) Department of Tumour Biology The Norwegian Radiumhospital 0310 Oslo E -mail: ingrid at microarray.no Phone: +47 22 93 54 11 Fax: +47 22 52 24 21