fold change question
I am trying to develop an estimate for the fold change in the expression level of a gene, under 2 conditions A and B. I take three signal intensity measurements in each condition, say, IntA(1), IntA(2), IntA(2) etc. The signal intensity provides a direct measure of expression level.
What is the best way to develop an estimate for the fold-change between A and B?
Two possible ways:
IntA(mean)= Mean of the 3 intensity measurements under condition A.
IntB(mean)= Mean of the 3 intensity measurements under condition B.
Mean fold change = IntA(mean)/ IntB(mean)
I calculate all 9 possible foldchanges: IntA(1)/IntB(2); IntA(1)/IntB(3); IntA(2)/IntB(1); IntA(2)/IntB(2) etc..
Then Mean fold change = Mean of the 9 fold changes.
Any feedback on which method is more suitable would be very much appreciated.
Thanks in advance!
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