I am a graduate student. Now I am doing ChIP with lymphocyte cell line derived from human.
so, I have duplicate ChIP data for each cell. Total number of data for 1 gene are going to be 12 because I have 3 control cells and 3 patient cells.
Since ChIP is performed to get certain protein occupancy at one gene with several primers that recognize several region of the gene, I have many data, and I am frustrated to get 'p value'.
Q is that what kind of statistics should I use?
I have 4 primer set that recognize 4 different region of my target gene (e.g. promoter, exon1, exon2, and exon3) in both 3 control cells and 3 patient cells. All experiment are duplicate..
I am thinking that I could use two-way ANOVA because I have two factors that can affect protein occupancy at my target gene ( control vs patient, dependant on region of target gene).
Moreover, I should show significance of protein occupancy between control and patient at certain region of target gene. how can I get it? I am thinking I should make one average bar out of 3 control cels and one bar out of 3 patient cells and do T-test??
Or..I am using Prizm two-way ANOVA and posttest option to get p-value b/w control and patient...
Am I right?
Or is there anybody who can help me?