Hi! I am interested in comparing expression of a particular single gene between metastatic osteosarcoma and non-metastatic disease. There are plenty of array data in GEO. I have downloaded the files, found the probe numbers and put down the intensities given by the probe speicifc to my gene of interest. As a reference, I put down the intensities for a number of classic housekeeping genes. This quick and dirty RT-qPCR-like preliminary analysis gave me some interesting results. How can I do this analysis properly?

Looking forward to your suggestions and tips.