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 <- segmentsm.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 This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.