[BioC] problem with LPE

[Phguardiol at aol.com]

Hi Nitin and all,
I m trying to use LPE to compare 2 groups. In first group I have 4 chips and in the second one 8 chips (same kind of CEL files, ie, HU133A from Affymetrix).
here is what I doing: 

library(affy)
library(LPE)
library(gcrma)

data1<-ReadAffy()
data2 <-gcrma(data1)
data3<-exprs(data2)
data4<-data.frame(Name=geneNames(data2), data3)
var.g1 <- baseOlig.error(data4[,2:5],q=0.01)   # group1 colum 2 a 5
var.g2 <- baseOlig.error(data4[,6:13],q=0.01)   # group2 colum 6 a 13

lpe.val1<-data.frame(lpe(data4[,6:13], data4[,2:5], var.g2, var.g1, probe.set.name=data4$Name))

And here is what I obtain first:
Warning messages: 
1: NaNs produced in: sqrt(1.57 * ((var.x/n1) + (var.y/n2))) 
2: NaNs produced in: sqrt(var.x) 
3: NaNs produced in: sqrt(var.y) 

then the following:

> lpe.val <- round(lpe.val1, digits=2)
> fdr.BH <- fdr.adjust(lpe.val, adjp="BH")
> fdr.2 <- fdr.adjust(lpe.val, adjp="resamp", iterations=2)
iteration number 1 is in progress
iteration number 1 finished
iteration number 2 is in progress
iteration number 2 finished
Computing FDR...
Error in "[<-"(`*tmp*`, j, value = z.real[num.genes.signif]) : 
        nothing to replace with
In addition: Warning messages: 
1: NaNs produced in: sqrt(1.57 * ((var.x/n1) + (var.y/n2))) 
2: NaNs produced in: sqrt(var.x) 
3: NaNs produced in: sqrt(var.y) 

When I look at the file I dont get any adjusted p values
any suggestion ?
thanks
Philippe

ps I ve been also trying the old version of LPE without permutation 
lpe.val1<-data.frame(lpe(data4[,6:13], data4[,2:5], var.g2, var.g1, probe.set.name=data4$Name, adjp=c("BH","BY")))

and obtained the same warning meesages: 
1: NaNs produced in: sqrt(1.57 * ((var.x/n1) + (var.y/n2))) 
2: NaNs produced in: sqrt(var.x) 
3: NaNs produced in: sqrt(var.y) 
and no adjusp P values