[BioC] Warning in mergeLevels

[Oscar Rueda]

Dear list, 

When running the mergeLevels() function from aCGH package with a long array
(for example:)

library(DNAcopy)
library(aCGH)
log2ratios <- rnorm(1440000)
Chrom <- rep(1:24, rep(60000, 24))
Pos <- rep(1:60000, 24)
CN <- CNA(genomdat=as.matrix(log2ratios, ncol=1), chrom=Chrom, maploc=Pos,
data.type="logratio", sampleid="test")
sm.CN <- smooth.CNA(CN)
y <- segment(sm.CN)
y.merged <- mergeLevels(log2ratios, rep(y$output$seg.mean,
y$output$num.mark))
 
A warning comes at the end:

Current thresAbs:  0.05
Warning message:
In m * n : NAs produced by integer overflow

This warning comes from ansari.test(), which is called by mergeLevels() and
seems to come from the multiplication of the result of the length() function
on the the logratios, which is an integer.
So the p-value returned is a NA, but after the calling to ansari.test(), the
code in mergeLevels does this:

if (is.na(ansari[j])) {
           ansari[j] = 0
       }

Now the p-value is 0 instead of whatever the value was if the multiplication
was properly done. 

What is the logic behind converting NA p-values to zero?

(Note that this problem can be avoided converting m and n to doubles in
ansari.test.default())

Best regards, 



Oscar M. Rueda, PhD
Breast Cancer Functional Genomics
Cancer Research UK Cambridge Research Institute
Li Ka Shing Centre 
Robinson Way 
Cambridge CB2 0RE 
England 




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