[BioC] issues with xps filter

[Larry N. Singh]

Hi everyone,

I'm having some issues with the madFilter in xps.  Please see below:

# Please note I've already loaded the RMA data in data.rma
preflr <- Prefilter(mad = c(0.25))
rma.pfr <- prefilter(data.rma, "tmp_prefilter", getwd(), 
filter=preflr, minfilters=1, logbase="log2")

tmp <- validData(rma.pfr)
d <- dim(tmp(tmp[, "FLAG"] == 1,])

> d
208 2

#### BUT

x <- validData(data.rma)
x <- log(x)/log(2)
mads <- apply(x, 1, mad)

> sum(mads > 0.25)
[1] 3641

I don't get the same numbers for MAD filtering.  
Can someone please tell me what I'm missing here?

Thank you kindly for any help.
-Larry.