I have used FFPE HNC samples in my study. I couldn't get FFPE non-cancerous samples. So, the calibrators were FF (fresh frozen) non-cancerous samples from different patients. Therefore, for calculating relative gene expression of FFPE HNC samples, the data were presented as the n-fold expression difference of each tissue relative to the calibrator sample. Fold expression was calculated by the formula 2-ΔCt.
Fold difference was calculated by the formulae:
Fold expression sample (2-ΔCt)FFPE /
Fold expression calibrator (2-ΔCt)FF(noncancerous)
where,
ΔCt sample= (Ct of targets - Ct of GAPDH)FFPE) and
ΔCt calibrator = (Ct of targets - Ct of GAPDH) FF non-cancerous
My way is to calculate relative quantity by the formula 2-ΔΔCt.
where ΔΔCt = ΔCt sample FFPE - avg ΔCt FF
ΔCt sample= (Ct of targets - Ct of GAPDH)FFPE
ΔCt FF = (Ct of targets - Ct of GAPDH) FF
After this mean of quantity FF non cancerous should be 1
Thank you very much, Alena, for sending the calculation.
Could you please direct me to some reading material or reference.
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