How to compute IP efficiency

[zhangmj]

When we got the data from chip-seq and normalized the total reads of two samples ,the expected same IP peak in two samples is different in intensity.It must come from the difference of IP efficiency. How to compute the IP efficency?Do someone have good idea? Did you see any paper give good method to solve this question?
Thanks!

[zhangmj]

the paper Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome used the normalization of IP efficiency .

[zhangmj]

any other ideas or papers?

[zwang0614]

If it is just from the IP efficiency, all the peak should have the same pattern. Then even you average these two samples' results, similar peak will also be obtained. In that case, why need to worry about the IP efficiency? I suppose you just wanna compare, rather than absolutely quantitation.