Hello all, The function `readPostitionalInfo` of 'snapCGH' package may contains a bug in this section: agilent = { split <- strsplit(input$genes$SystematicName, split = ":") chr <- start <- end <- vector(length = length(split)) for (i in 1:length(split)) { if (length(split[[i]]) == 1) { chr[i] <- start[i] <- end[i] <- NA } else { chr[i] <- substr(split[[i]][1], 4, 5) if (chr[i] == "X") chr[i] = 23 else if (chr[i] == "Y") chr[i] = 24 temp <- strsplit(split[[i]][2], "-") start[i] <- temp[[1]][1] end[i] <- temp[[1]][2] } } } The purpose of these codes is to extract the positional information of probes from the "SystematicName". The SystematicName of probes are like "chr1:12345-45678", then here "chr" should be 1, start 12345, end 45678. But there are many other forms of SystematicName, like: 1. chrUn:123-456, which will be converted to 'NA' with chr; 2. chr1_random:123-456, which will be converted to 'NA' with chr; 3. chr10_random:123-456, which will be converted to '10' with chr; 4. chrX_random:123-456, chrY_random:123-456 and chrUn_random:123-456, which will be converted to 'NA' with chr; 5. chrM:123-456 and chrM_random:123-456, which will be converted to 'NA' with chr; Based on these considerations, I think this piece of code needs some modifications. Best wishes! -- Zhi-Qiang Ye Ph.D in Bioinformatics