samr package: missing values in RNAseq data

[Vickie S]

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
     
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