In a permutation-based t-test analysis output, to what parameter the False Discovery Rate column corresponds to?
It`s obvius it doesn't correspond to the FDR value itself, as the FDR is an only value for all the analysis (the estimated proportion of false positives) and not a parameter calculated for each gene. So, what's that exactly? A corrected p-value for the gene?
Thanks for your attention.
The false discovery rate column corresponds to the false discovery rate given a cutoff corresponding to that gene's p-value.
In other words, if you had run the analysis with a cutoff equal to that gene's p-value, the estimated proportion of false positives would be the value seen in the False Discovery Rate column.
Hope that helps,
Thanks for your answer.
The problem is that after setting the threshold in p<0.01; and FDR<0.15 with 15000 permutations, in the output, the highest values of p-values and FDR of the significant genes don't correspond to thresholds I established (they vary between 0.00004<p<0.003 and 0.022<FDR<0.0026) and this has happenned to me several times. I'd like to understand that.