In my experiment, I have 8 experimental groups (n=8 rats); one control and 7 treatments. I have performed an OpenArray for each group, so I have 8 OpenArrays. In each OpenArray I have included 112 genes with 7 endogenous genes, as I have 3 tissues (liver, fat and colon) there are 2 endogenous genes per tissue.
At the end, I have the expression of 112 genes per tissue and per rat.
I would like to know how to analyze this data, since I haven't found any information on internet.
My idea was to analyze the data using the 2^(-deltadeltaCT) method as in a regular RT-qPCR. Comparing each rat with the control group and in each tissue. In each tissue, I would use the best endogenous control.
Thanks in advance,
Alex