Description
Hi Weixu,
I am using ENIGMA to estimate cell fraction to estimate cell type-specific gene expression. I created an ENIGMA object using the 'single_cell' type, where the bulk is a matrix with 971 samples and 28,285 genes, and the reference is from 10 other samples, containing 12,506 cells and 28,285 genes. However, when I use the created ENIGMA object with the RLR method to estimate cell fractions, it shows that the program needs three days to run (ncores=5). I would like to ask if this is normal.
At the same time, I tried selecting 20-1000 genes in the Reference to get results faster. But an error occurs: Error in rlm.default(x, y, weights, method = method, wt.method = wt.method, : 'x' is singular: singular fits are not implemented in 'rlm'.
Kindly regards,
Zhao