Hi guys, I tried to use SVA package to identify number of batch factors in my gene expression dataset. But I ran into an error message: > library(sva) > load("myeset.RData") > pheno <- pData(myeset) > str(pheno) 'data.frame': 821 obs. of 4 variables: $ sample : Factor w/ 821 levels "A_837766__U133Plus2",..: 1 2 3 4 5 6 7 8 9 10 ... $ Source : Factor w/ 6 levels "C1","C2",..: 5 5 5 5 5 5 5 5 5 5 ... $ CancerType: Factor w/ 28 levels "Anus","Bladder",..: 10 14 14 10 10 14 14 14 11 14 ... $ Batch : Factor w/ 14 levels "20110909_U133Plus2",..: 1 1 1 1 1 1 1 1 1 1 ... > edata <- exprs(myeset) > str(edata) num [1:18960, 1:821] 4.98 4.95 8.29 4.21 2.9 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:18960] "100009676_at" "10000_at" "10001_at" "10002_at" ... ..$ : chr [1:821] "A_837766__U133Plus2" "A_937608__U133Plus2" "A_949340__U133Plus2" "A_949363__U133Plus2" ... > > mod <- model.matrix(~as.factor(CancerType), data=pheno) > mod0 ~ model.matrix(~1,data=pheno) mod0 ~ model.matrix(~1, data = pheno) > n.sv = num.sv(edata,mod,method="leek") Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays Any suggestion? Thanks a lot, Ying > traceback() 1: num.sv(edata, mod, method = "leek") > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] splines parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pamr_1.54.1 survival_2.37-4 cluster_1.14.4 bladderbatch_1.0.5 sva_3.6.0 mgcv_1.7-24 corpcor_1.6.6 [8] Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] grid_3.0.1 lattice_0.20-15 Matrix_1.0-12 nlme_3.1-110 tools_3.0.1 > Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:14}}