I downloaded TCGA breast cancer methylation data from 91 female individuals but I found something interesting. The data of female annotated by 'hg38' have Y chromosome gene symbol.
So, I searched how to handle it and get solution that tells to use reference 'hg38 canonical female'. the difference between hg38 and hg38 canonical female is as below:
(1) The hg38 contains all chromosomes as well as all unplaced contigs.
(2) The hg38 canonical female contains everything from the canonical set with the exception of chromosome Y.'
then, is it the same as removing the Y chromosome from the data annotated with hg38?