[BioC] issues with xps filter
Larry N. Singh
larryns at pcbi.upenn.edu
Wed Jun 30 19:01:29 CEST 2010
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,])
x <- validData(data.rma)
x <- log(x)/log(2)
mads <- apply(x, 1, mad)
> sum(mads > 0.25)
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.
More information about the Bioconductor