I am trying to find differentially expressed genes in my RNA-Seq data. I have noticed that based on the count matrix I provide, whether it contains only the direct comparison or more of the data, I get different p-values.
For example: I am comparing (0.5h stimulated to 0.5h unstimulated) and (1.0h stimulated to 1.0h unstimulated). 1) I can provide a count matrix which has counts for all four conditions. Then, I look at the p-values for 0.5 stimulated vs 0.5 unstimulated. OR 2) I can provide a count matrix which only has the counts for the conditions I am directly comparing ( 0.5h stimulated vs 0.5h unstimulated). When I compare the p-values between the two methods they do not match.
I am wondering which is better/ more accurate/ more true to the data?