I am running deconvolution on a PBMC bulk RNA sequencing data in R. The problem is that I get very different results when using different methods: quantiseq CIBERSORT EPIC ABIS
Besides EPIC it seems that most methods are having difficulty characterizing the cells fractions. I would expect that a well established method would be able to recognize a PBMC data and therefor I won't have a large fraction of cells which are uncharacterized when using appropriate reference matrix.
How can I tell which method yields the best result?
Does anyone have an experience with one of the methods on PBMC/in general?
All the best