This appears to be the case even in breast cancer cell lines. Could this be an overcorrection resulting from the minuscule relative copy number values associated with zero chrY copies?
Thanks for posting this! It’s in the queue of things to investigate.
Hi ralkallas,
Upon investigation, we noticed that copy number correction is causing Y chromosome genes to have a abnormally high gene effect. Chronos copy number correction occurs relative to the overall mean gene effect. Due to frequent copy number loss of the Y chromosome, the overall uncorrected mean gene effect of chromosome Y genes were distorted, causing the copy number corrected gene effects to be positive. We will be addressing this problem in the upcoming 26Q3 release. Thank you for bringing this to our attention.
