Dear all,

Thanks for reading. I know that this issue has been discussed many times, but I am not able to find the right solution to it. I have read other posts and the vignette, I have changed the .CEL files number (10. CEL, 50. CEL, >100.CEL) and the same error keeps popping up. I guess that specifying na.rm=TRUE could change things, but I have no clue where to specify it. 

> library(ff)

> library(genefilter)

> library(IRanges)

> library(MASS)

> library(VanillaICE)

> library(crlmmCompendium)

> library(oligoClasses)

> library(crlmm)

> ocProbesets(50000)

> ocSamples(200)

> filenames<-list.celfiles(full.names=TRUE,pattern=".CEL")

> plate<-substr(basename(filenames), 19,26)

> cnSet<-genotype(filenames=filenames, cdfName="genomewidesnp6", batch=plate, gender=2)

Loading required package: genomewidesnp6Crlmm
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Loading annotations and mixture model parameters.
Initializing ff objects.
Instantiating CNSet container
Preprocessing 12 files.
Error in quantile.default(M, c(1, 5)/6, names = FALSE) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE

Thanks for your time and patience.

Inigo