I performed a transcriptome analysis (Clariom D Array, Affymetrix) of two groups of subjects (human tissue) by using Transcriptome Analysis Console (TAC; Affymetrix) and Partek software and same cutoff (n=20; FC greater than 1.5 and P value less than 0.05). However, the overlap between differential expressed genes between both software was quite low.
someone has some comment about why this may be happening?