Hi Jen,

The way Conn applies FDR correction is seed based. For a given seed (say 381), all the target connections' p values will be considered when calculating the FDR cut-off (q value). Vice-versa when looking at 89, the cut-off will be based on the p values obtained from all the p values when considering 89 as the seed. Therefore, it is quite possible that 381-89 is significant but not 89-381 as the correction is dependent on the actual values when considering each of these as a seed.

Here is an older forum post about this: https://www.nitrc.org/forum/message.php?...
and here is a link to a detailed reply from Dr. Alfonso: https://www.nitrc.org/forum/message.php?...


Hope these help

Best
Pravesh