Permutations and RASQUAL results

[SaideepGona]

Hello,

Just want clarity on exactly what the outputs mean. My understanding is that the chi-square statistic comes from the likelihood ratio test, and thus can be converted to raw pvalues directly. What is the relation to the Q-value output?
Also, what exactly is the permutation test doing? And is it related to what is reported in the online methods multiple testing correction section?

Thanks!

[SaideepGona]

updates on this?