In case of an unbalanced number of samples per group, the standard DESeq outlier replacement (minReplicatesForReplace=7) can result in drastically reduced p-values. This happens when the trimmed mean replacement leaves out all samples from the smaller group. See the following example:
First two values belong to the smaller group. The last value (larger group) is replaced by 154:
1272, 751, 275, 298, 113, 116, 161, 176, 294, 172, 327, 93, 108, 84, 151, 728
I am aware that unbalanced groups and small sample numbers should be avoided, but this happens quite often in reality ;-). I would prefer having the outlier replacement deactivated by default or a check for unbalanced groups...