I want to measure the expression of a target between two conditions such as cancer vs normal. To achieve this, which method is ideal, i.e. whether absolute quantification or relative quantification?
Relative quantification will be enough here - unless you want to know how many ampiliable target molecules are in a cell (provided you can precisely count the number of cells used; possibly adjusting for RT efficiency using some calibrator-RNA...)
I would have used relative, it will give you a good enough answer and is based only on the relative expression of your gene of interest compared to a reference gene in treatment vs control. However, I've spoken to some qPCR developers, who assure me that absolute quantification is far superior - given that you still have the inherent comparability between conditions but with an additional normalization of a standard curve. I think this may have something to do with the fact that you will end up using significantly more of the dye products they want to sell though. As long as you validate the primers with a standard curve first relative is fine.
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