I am in a basic level of statistics and using DESeq package for RNA-seq. I don't understand how DESeq calculates p-value exactly. If we simplify statistics, for two sample mean comparison we either use z-test or t-test, right?
How about in DESeq?
In DESeq paper :
H°: qiA = qiB means Hª: qiA != qiB
KiA = sum(Kij) , KiB = sum(Kij)
Pi = sum p(a,b) / sum p(a,b) //sorry I couldn't write the notations well as there is no enough options here.
1- So please someone can explain how this can be calculated?
2- Does DESeq use Negative Binomial to estimate Mean and Varience then plug these two in t-test to calculate p-value?
Thanks for any useful info. Through your answers, we can discuss it more.