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In my opinion you should use this formula: $\huge \frac{log_2(Iso_1/Iso_2)}{log_2(GAPDH)} $ This will normalize the relative fold differences between the isoforms with the loading control- GAPDH. Since both numerator and denominator are log transformed they are in comparable domains unlike the formula-2 that you mention in your question. This is just a ...

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