CummeRbund csVolcano() alpha and pvalue questions
I've got a couple questions about csVolcano().
I've tried plotting with alpha = 0.05, and showSignificant = TRUE. When I look at the red data points, the lowest they go is about 2.75. But then log_10(0.05) is about 3 (far enough from 2.75 that I know it isn't right). Then I tried alpha = 0.01, and the lowest red points are around 3.7. log_10(0.01) is around 4.6 though. Is the y axis not really log_10(p value)? Or maybe I'm just misunderstanding the relationship of alpha and p value. I was under the impression that if the p value is less than alpha, then we reject the null hypothesis, i.e. accept that there is significant change. Is this correct?
Thanks,
Blake
