Reference for qPCR Chip? - (Mar/15/2010 )

Hi!
I'm doing ChIP on plants (arabidopsis) , and I have to validated the CHIP by qPCR. (Yeah after ages of optimisation !!)
I cheked my pull down with normal PCR it's fine, I've tested my primers for positive and negative control for my region of interest by normal PCR and they works well... so now I' ready to run qPCR.

It's my first time on Chip sample, usually I made that on cDNA samples, and for that I know that I have to use a reference gene (as Actin, UBQ10 etc). Do I need the reference for the ChIP as well? I mean If I use the normalization method of % of input Is that necessary??
Nobady report nothing about that in the methods of papers!!!

Thank you!!!

As far as I can tell everyone does something different. Some people specific/mock. Some just % input. Some normalized to percent input of a "control" region. Some %input then fold change over some control group. So I guess it depends on your reviewers which one you end up using! I wish I had an answer. For what it's worth I intend to use % input then do fold change over my control group, unless of course I get a reviewer that requests otherwise...

MM