[BioC] Limma for GoldenGate Methylation Cancer Panel I

[Jinyan Huang]

Does anyone have the exprience to use limma for two-color array:
GoldenGate Methylation Cancer Panel I (Golden Gate Cancer Panel
Methylation Illumina)

I used it to analysis Methylation data for finding the different
methlated genes, but the result is not good. There are too many small
p-value the result. there are biology repeat in my data. My R code is
like this:

library(limma)
exp<-read.table("exp.txt",F)
sample_id<-read.table("sample_id",F)
row.names(exp)<-exp[,1]
exp<-exp[,-1]
design<-read.table("design.txt",F)
explow<-exp[,design[1,]==-1]
exphigh<-exp[,design[1,]==1]
expsort<-cbind(explow,exphigh)
idlow<-sample_id[design[1,]==-1]
idhigh<-sample_id[design[1,]==1]
idsort<-c(idlow,idhigh)
colred<-rep("red",length(exphigh[1,]))
collow<-rep("blue",length(explow[1,]))
col<-c(collow,colred)
MA<-as.matrix(expsort)
exp_norm<-normalizeBetweenArrays(MA,method="scale")
design_sort<-c(rep(-1,length(collow)),rep(1,length(colred)))
fit <- lmFit(MA,design_sort)
fit <- eBayes(fit)
mylist<-topTable(fit,number=Inf,adjust="BH")