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I'm trying to repeat sva function using sva package following the vignettes (October 2014).
library(sva) library(bladderbatch) library(pamr) library(limma) data(bladderdata) pheno = pData(bladderEset) edata = exprs(bladderEset) mod = model.matrix(~as.factor(cancer), data=pheno) mod0 = model.matrix(~1,data=pheno) n.sv = num.sv(edata,mod,method="leek") n.sv [1] 2
why i got 2 not 4?
Thanks
-Shirley