How to calculate an "Effect size" from WASP CHT output

[blake-bowen]

Hi,

I was wondering, do you have a recommendation for how to calculate the effect size for CHT results?

Would something like the following work, using the alpha and beta maxiumum likelihood estimates output from the CHT combined test to calculate an allelic fold change?

allelic_fold_change = log2(beta/alpha)

Thank you,
Blake

[gmcvicker]

Yes, you can calculate an effect size using the log2 ratio of alpha and beta as you suggest (or any similar statistic that compares alpha and beta).