What kind of normalization to do when plotting aggragate plot using two different chip-seq bam files

[Shawn Bai]

Hi, all, 

I have two samples of Chip-seq experiment, one treated with DMSO and another treated with a drug, I want to compare the two on enhancers, so I will plot an aggregate plot on the enhancer regions using the two chip-seq file using ngs.plot.r. but the two files must have different sequencing reads, I am wondering what kind of normalization is needed for the two files? Or ngs.plot.r can normalize itself when plotting the figures. Thanks!