I am using the removebatcheffect function with simulated dataset using rnorm in order to test it. So i have one experimental factor with two groups and one batch effect with 2 groups. The design is complet and balanced. The correction seems to work well when i visualizing data on boxplot before and after correction but i dont understand why fold-changes between my two experimental groups before and after are the sames.
I tried the function using only the batch argument and also with the design argument but fold-changes are the sames each time.
Did anybody observe this using these function ?