comparative quantitation - (Sep/30/2008 )
I compare several candidate reference genes with each other with geNorm. The requirred quantaties I optain with the Comparative Quantitation Analysis tool implemented in the Corbett Rotor Gene software. The quantaties of each gene are measured relative to a calibrator and are based on individual take off values and reaction efficiencies.
On my search for outliers I realize that the relative quantity of gene 1 varies if I toggle gene 2 on or off. How can this be? It should not be affected by gene 2 if it is quantified only by it's own efficiency, take off value and the calibrator. I also wrote to Corbett, but mybe someone here also knows the answer.
Well I can give the answer now myself,
the comparative quantification tool from Corbett calculates the quantaties with the average reaction efficency of all samples not only with the one for a specific gene, allthough this is also calculated but just not used.
all the best