Hi Folks,
I have two treatment conditions on a mouse cell line and I would like to know which treatment works better than the other one. For that, I will compare these two treatments' regulators and biological pathways. One of the possibilities is to have separate analyses for each treatment and then compare the regulators and biological pathways together. The other possibility (I am not sure if I am correct or not and I need your brain to help me), is that I calculate the differences of logFC between treatment and B (LogFCA-LogFCB) or take the ratio (Log2FCA/Log2FCB) and then look at what biological pathways or regulators could be activated by the differences between differential expression of two conditions. Please let me know if you have any suggestions or ideas and if you think is OK, what difference is more valuable, subtracting LogFCA-LogFCB, or the ratio of two conditions (LogFCA/LogFCB)?
Thanks, M
