Dear all, Hi! I wonder, for aCGH data analysis, what is the threshold cutoff values or criteria used to call gain, amplification, loss, and deletions? I know some might use arbitrary numbers as thresholds but I am curious about whether there is a better way to take into account case by case. In case, all my data are cancer samples without normal samples as references, what could be the best way to infer the threshold values to call aberrations? Shall I take the mean copy number of all probes across all samples to use it as the backgroun or if I have a target gene, and I can just take the mean copy number of the probes against this target gene across all samples? Thank you so much for your help in advance! Sincerely, Allen [[alternative HTML version deleted]]