Hi All, As mentioned in the manual of SAMseq function of samr package,? missing values in the data are allowed in the input data matrix. "x-- Feature matrix: p (number of features) by n (number of samples), one observation per column (missing values allowed)" When I try a matrix with missing values, I get the following error: SAMseq(counts(cset), cset$cond1, resp.type =? "Two class unpaired",geneid = featureNames(cset), genenames = featureNames(cset), nperms = 100, nresamp = 2 , fdr.output = .05) Estimating sequencing depths... Error in quantile.default(prop, c(0.25, 0.75)) : ? missing values and NaN's not allowed if 'na.rm' is FALSE It seems like there is an inbuilt quantile normalization function. Though i don't know how to debug this error. I also like to receive any suggestion about interpretation of missing count values in the matrix. Any idea ? cheers, Vickie S