I am confuse if padj and FDR is same? I am in the mid of analysis and confused if I have FDR or not. I have seen some explanation but not able to get the answer.  please share your views.
Thanks
The "false-discovery rate" is the fraction of positives that are false positives at a given p-value threshold. It is a property of the threshold, not a property of a gene. So, if you do a 1000 tests, and get 100 positives at p<0.05, your FDR is 50% (as 50 false positives would be expected in 1000 tests at p<0.05). 

Thus, technically speaking, it doesn't make sense to say a gene has an FDR. This is why many tools will use the term "adjusted p-value" or "q-value". The adjusted p-value is the FDR your experiment would have if you set the threshold at the p-value for this gene. Thus, in our example above, a gene with a p-value of 0.05 would have a padj/qvalue of 50% because if you set the threshold at 0.05, you would have a 50% FDR.
