Off topic:p-value using moderated t test
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gv ▴ 40
@gv-6516
Last seen 18 months ago
United States

Hi,

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!!

limma p-value r FDR • 258 views
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