I was creating a new scater object with a list of 20K genes. After the new sce object is created, the gene list was automatically reduced to ~2K genes. Is this by default? How can I fix it to incorporate all 20K genes?
You're going to have to be more specific. What is your code? What functions are you using? What version of scater are you using? The latest version doesn't even support SCESet objects, you should be using SingleCellExperiment instead.