[R] samSeq and poissonSeq - quantile.default error

jiag at ece.ubc.ca jiag at ece.ubc.ca
Fri Feb 14 23:05:24 CET 2014

Dear all,

I have a RNA-seq cancer dataset (2 classes) with all raw integer counts,
does NOT contain any NaN or missing value.

When I run samseq and Poission-seq, I got the following error:
"Error in quantile.default(prop, c(0.25, 0.75)) :
  missing values and NaN's not allowed if 'na.rm' is FALSE "

Does anyone know how to fix this problem?
Thank you,

I've tried the following:

In samr, I tried to change
depth = samr.estimate.depth(x) to
depth = samr.estimate.depth(x, na.rm=TRUE)
which didn't work.

In samr.estimate.depth, I also tried to change
qs <- quantile(prop, c(0.25, 0.75)) to
qs <- quantile(prop, c(0.25, 0.75), na.rm = TRUE)
which didn't work either.

My code to call samseq:
y <- c(rep(1, 27), rep(2, 22))
output = SAMseq(x, y, resp.type = "Two class unpaired",nperms = 100,
random.seed = NULL, nresamp = 20, fdr.output = 0.05, na.rm = TRUE)

code to call PoissonSeq:
y <- c(rep(1, 27), rep(2, 22))
type <- "twoclass"
pair <- FALSE  #not matched-pair design

dat <- list(n=x, y=y, type=type, pair = pair)
para <- list(npermu=100, seed=10) #default params
output = PS.Main(dat=dat, para=para)

More information about the R-help mailing list