Closed caravagn closed 3 years ago
I mean, all genes in DE_table
should have a mapping in x$data$gene_locations
no?
Here the situation is a bit tricky. Basically you are testing DE on a lot more genes that the ones you use in the CONGAS analysis. The main reason is that not all the genes you have in the expression matrix map to a valid segment (either because your segmentation is incomplete or too fragmented in a specific position). Other genes may be filtered in the pre-processing step; however, you would ideally like to include everything in the DE analysis.
Problem:
DE_table
contains many genes, when I subset given gene locations I loose multiple genes. There is some problem with the way genes are stored across the various data structions