I was need some advice on how to present some aggregate plot data. I have 2 categories of genes that I want to analyze. When I look at the enrichment at the TSS of these 2 gene categories for a factor from a ChIP-Seq data set I get the following result.
The plot shows Log 2 transformed input normalized (as performed by NGS.plot.r) factor read density at the TSS of gene category A and B. I would like to further normalize for the differences in the base line, to show that the genes in category B have more of the factor present relative to the surrounding baseline. How can one do this?
Alternatively, is it not legitimate to normalize out the base line. Do I need to show it as is?