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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