samr package: missing values in RNAseq data

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