[BioC] Fwd: SAFE with small sample sizes

[Ina Hoeschele]

Hi all,
   I am now running SAFE with a user-defined function for the local statistic (to get the limma statistic) but I am still getting the error message below. I tried several other versions and using args.local, but no matter what I do I get the same error message. Any suggestions?
Many thanks ... please see below.

local.Limma <- function(X.mat,y.vec) {
	t <- rep(0,33105);
	design <- cbind(MU=1,TvsC=y.vec) 	
	fit <- lmFit(X.mat,design)
	fit <- eBayes(fit)
	t <- fit$t
	t <- t[,-1]
	return(t)
}

library(safe)
library(multtest)
y.vec <- c(rep(0,nsmpl1),rep(1,nsmpl2))
safe(X.mat=Mdata,y.vec=y.vec,platform="canine2.db",annotate="KEGG",Pi.mat=1,local="Limma",global="Wilcoxon",error="none",alpha=0.05,method="permutation",min.size=10)

Building KEGG categories from canine2PATH
  Categories completed:20% 40% 60% 80% 100% 
  186 catgories formed
Error in get(paste("local", local, sep = "."))(X.mat, y.vec, args.local) : 
  unused argument(s) (args.local)