Real-time PCR statistics help!

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eej28's picture
Real-time PCR statistics help!

I have a question regarding how to do statistics on real-time PCR data.

Let's say I am treating cells with inhibitor X and measuring expression of gene Y, and I want to see if induction of gene Y by some stimulus is reduced by inhibitor X. Let's say I repeat this experiment 5 times, independently, and get the following results, expressed in fold-induction by the stimulus:

untreated: 10, 20, 15, 12, 8
+ inhibitor X: 5, 6, 9, 4, 7

Do I do a t-test based on the fold-change values? i.e. [10, 20, 15, 12, 8] vs. [5, 6, 9, 4, 7]

Or, do I do express the inhibitor data set as a % of the untreated and do a t-test based on [100%, 100%, 100%, 100%, 100%] vs. [50%, 30%, 60%, 33%, 87.5%]? Assuming the data set is paired.

I have also heard that it is more accurate to do statistics based on the delta-Ct values from real-time PCR and not the fold-change data. Any thoughts on this?

Apologies if this is a silly question. Thanks!


Biju's picture
Hi eej28

Hi eej28
You could do paired 't' test either way as you suggested depending on your interest and how you want to present  data in presentations/publications.

Delta Ct method  will be helpful in analysisng data when the standard curve obtained in different runs are not consistent . In this case dela Ct method is useful.
Biju Joseph