We regret the fact that you have decided to terminate your fellowship in the group here and that your research experience did not tum out in a way that you found to be positive. We also appreciate your concerns about the nature of the work and the approaches taken to the problems. While we disagree with some of the measures you suggest should be taken to address the issues raised, we do recognize that there are some areas of the work that were less than perfect and need to be rectified.
I suspect that we likely disagree with what constitutes validation.
We recognize that you are concerned about some of the methods used to develop predictors. As we have discussed, the reality is that there are often challenges in generating a predictor that necessitates trying various methods to explore the potential. Clearly, some instances arc very straightforward such as the pathway predictors since we have complete control of the characteristics of the training samples. But, other instances are not so clear and require various approaches to explore the potential of creating a useful signature including in some cases using information from initial cross validations to select samples. If that was all that was done in each instance, there is certainly a danger of overfitting and getting overly optimistic prediction results. We have tried in all instances to make use of independent samples for validation of which then puts the predictor to a real test. This has been done in most such cases but we do recognize that there are a few instances where there was no such opportunity. It was our judgment that since the methods used were essentially the same as in other cases that were validated, that it was then reasonable move forward. You clearly disagree and we respect that view but we do believe that our approach is reasonable as a method of investigation.
……We don’t ask you to condone an approach that you disagree with but do hope that you can understand that others might have a different point of view that is not necessarily wrong.
Finally, we would like to once again say that we regret this circumstance. We wish that this would have worked out differently but at this point, it is important to move forward.
The Med Student’s Memo
Bradford Perez Submits His Research Concerns
Nevins and Potti Respond To Perez’s Questions and Worries
A Timeline of The Duke Scandal
The Cancer Letter’s Previous Coverage
I’ll put this up in my regular blog shortly