I have two different cancer cell lines (EJ28 and TCCSUP) that are persistently infected with virus and called them EJ28Pi and TCCSUPPi respectively. So, I performed RNA-seq analysis for each cell line versus its control (for example EJ28Pi VS EJ28) differently using DESEq2 package from R.
Now I want to perform global expression between the two cell lines. The question is how can I do this?, am I to combine the triplicate of both EJ28Pi VS EJ28 and TCCSUPPi VS TCCSUP together in a single analysis or I should just combine the triplicate of EJ28Pi VS TCCSUPPi? I am a bit confused here. So, I need the true meaning and brief explanation of Global Transcriptome Analysis in my case using my samples above.
Thank you for your usual support.