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Your qPCR run is done and you have a column of Ct values. Here is how to turn them into fold changes with the ΔΔCt method, worked by hand, in a spreadsheet and in R, plus the mistakes that get qPCR figures sent back by reviewers.
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If you test 20,000 genes at once, you’ll get 1,000 "significant" results by chance alone. This post explains the Multiple Testing Problem and how to use the p.adjust() function in R to calculate False Discovery Rates (FDR) and protect your results.
