ChIP data interpretation and representation - (Mar/08/2010 )

Hi,
I would need help to interprete and analyze my data. I have done a ChIP using magnetic beads..... I have a positive control ab (H3) 2 ab of interest (H3K4 and H3K27 m3) and my negative control IgG..... now on these sample I did a qPCR.... the problem is that I have strong signal differences between my samples (percentage of h3K4m3 for GAPDH 5, for GOI 0.1 negative control 0.3) . To analyze the data I use two methods: IMHO with fold change and the classic % of input. My question is: is it normal?? my I use a log scale to visualize the data? Thank you in advance for your help......

sorry I wanted to say H3 and not h3k4m3, i have strong differences between the samples in the positive and negative controls