I have an input file which looks like this:
Junctions s1_1 s1_2 s2_1 s2_2 junc1 0.23 0.25 0.76 0.78 junc2 0.27 0.31 0.51 0.50 junc3 0.9 0.78 0.16 0.12
Column1 are the junction coordinates. Column 2 and 3 represent percent splice in(psi) values for sample1(replicates). Column 4 and 5 represent percent splice in(psi) values for sample 2(replicates)
Each row defines one event. I want to calculate a p-value(significance) for each event. That is, is the event significant, meaning event for sample2 is up or down regulated w.r.t sample 1.
Can I use moderated t-test from limma package for this? Any other recomendation to calculate a p value?
Thanks for the help!!