Q-value and local FDR

[xgt1986627]

In the early version, there isn't local FDR showed in the result page. But in the latest version, local FDR appeared and the value of it is not the same with q-value. I found their meaning are the same in publication. Why they are different in latest EDGE and which should I use to judge whether the gene or protein is significant?

[ajbass]

The old EDGE package is no longer maintained. See http://genomine.org/papers/Storey_FDR_2011.pdf for more on the q-value/local false discovery rate.