[BioC] aCGH package analysis - duplicate spot averaging problem

[Ian Roberts]

Dear All,

I've recently gotten to grips with aCGH analysis using snapCGH and aCGH 
packages.  All is now going well, except in aCGH (Jane Fridlyand) I'm unable to 
get the acgh.process command to run with duplicate removal = TRUE.

It works if dupRemoval is set to False

This is what I get:
#> ex.acgh<-aCGH.process(ex.acgh, chrom.remove.threshold=23, prop.missing=0.25, 
sample.quality.threshold=0.4, unmapScreen=T, dupRemove=TRUE)

Averaging duplicated clones
CTB-102E19       4656 4657 

Error in `[<-.data.frame`(`*tmp*`, ind1[j], , drop = FALSE, value = c(-
0.156355155,  : 
        unused argument(s) (drop = FALSE)
#>

Would be grateful if anyone has any tips on how to handle duplicate clones in 
aCGH.

Thanks very much.
Ian