Powering on the per-protocol set

Generally speaking we power based on the per-protocol set and then increase the sample size requirement to give the number required in the full analysis set. Under some circumstances, for example in anti-infective trials, we factor up further to take into account the patients that are recruited, but are not eligible for the full analysis set. 

In a similar way it may be that the crd seen in the analysis based on the per-protocol set is larger than that seen in the full analysis set and this anticipated difference may also need to be factored in. 

It must be noted, however, that even if the sample size calculation gives enough power for the per-protocol analysis the potential for bias in that analysis still remains. 

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