I'd like to perform a deconvolution on my bulk RNA seq data. I'm testing CIBERSORT as an option.
Is the VST transformation on raw counts appropriate for use as CIBERSORT input? It is said that the data used as input should not be log-space normalized
If VST is not appropriate how can I actually normalize the data appropriately?
Since it is declared by CIBERSORT it seems that it is more appropriate for Chip data rather than RNAseq. Does anyone know an validated alternative (maybe a good R package)