I am trying to figure out CIBERSORT for RNA-Seq data. I have 5 control samples and 32 patient samples. I have DeSeq2 outputs and count data.
I have 2 questions.
1.Should I use DeSeq2 outputs as input to CIBERSORT for Impute Cell Fractions mode or just should I use count data obtained from Featurecounts?
2.Should I include control group data into input file or just patient's data