[BioC] Has anyone successfully used sva packages?

[Fabrice Tourre]

Dear list,

Fellow the paper "Tackling the widespread and critical impact of batch
effects in high-throughput data" and the code at
http://rafalab.jhsph.edu/batch/, I used sva in my analysis. But I
always get more than 90% of gene with p.adjust<0.05 (compared in two
cell line). When I try limma package without sva, it give me about
3000 genes with p.adjust<0.05. It seems limma is reasonable. But it
seems that limma can only remove tow batch each time using
removeBatchEffect.

removeBatchEffect(x,batch,batch2=NULL,design=matrix(1,ncol(x),1))

Does anyone have suggestions?

library(preprocessCore)
#cel=read.csv("celfies/cel_files.txt",header=F,skip=1)
tab=read.table("output/ExpressionInput/groups.dis.txt",as.is=TRUE)
mat<-read.table("gene/apt/rma-sketch.summary.txt",check.names =
FALSE,header=T,row.names=1)
colnames(mat)->c
rownames(mat)->r
merge(c,tab,by.y=1,by.x=1)->b
tab<-b
mat<-normalize.quantiles(as.matrix(mat))
colnames(mat)<-c
rownames(mat)<-r
dates=vector("character",ncol(mat))
for(i in seq(along=dates)){
	tmp=affyio::read.celfile.header(file.path("celfies",tab[i,1]),info="full")$ScanDate
	dates[i]=strsplit(tmp,"T")[[1]][1]
}
dates=as.Date(dates)
batch=as.numeric(dates-min(dates))
batch=as.numeric(cut(batch,c(unique(batch),1)))
batch[is.na(batch)]=1

library(corpcor)
library(affy)
library("sva")
library(limma)
f<-factor(tab[,3])
mod = model.matrix(~f)
mod0=model.matrix(~1,data=tab)
colnames(mod)<-levels(f)
n.sv = num.sv(mat,mod,method="leek")
svobj = sva(mat,mod,mod0,n.sv=n.sv)
modSv = cbind(mod,svobj$sv)
mod0Sv = cbind(mod0,svobj$sv)
pValuesSv = f.pvalue(mat,modSv,mod0Sv)
qValuesSv = p.adjust(pValuesSv,method="BH")

fit = lmFit(edata,modSv)
contrast.matrix<- ???? How to construct this matrix?
fitContrasts = contrasts.fit(fit,contrast.matrix)
eb = eBayes(fitContrasts)
topTableF(eb, adjust="BH")




head(tab)
                     x V2  V3
1 2A6_Hex_07Jul_09.CEL  1 dis
2 2A7_Hex_07Jul_09.CEL  1 dis
3 2A8_Hex_07Jul_09.CEL  1 dis
4 2A9_Hex_07Jul_09.CEL  1 norm
5 2AA_Hex_07Jul_09.CEL  1 norm
6 2AB_Hex_07Jul_09.CEL  1 norm