Forensic bioinformatics

The October 2008 issue of AMSTAT News has an article entitled “Forensic Bioinformatician Aims To Solve Mysteries of Biomarker Studies.” The article is about Keith Baggerly of M. D. Anderson Cancer Center and his efforts to reproduce analyses in bioinformatics papers.

The article quotes David Ransohoff, professor of medicine at UNC Chapel Hill, saying this about Keith Baggerly.

I think Keith is doing a wonderful and needed job … But the fact that we need people like him means that our journals are failing us. The kinds of things that Keith spends time finding out — what [the researchers] actually do — that’s what methods and results are supposed to be for in journals. … We need to figure out how to do science without needing people like Keith.

One of the reasons for lack of reproducibility is that journals press authors for space and so statistics sections get abbreviated. (Why not put the full details online?) Another reason is that bioinformatics articles are inherently cross-disciplinary and it may be that no single person is responsible for or even understands the entire article.

One thought on “Forensic bioinformatics

  1. Sheikh

    Mark: It is not only design of emperixents (DOE), and checking assumptions, that are routinely ignored in the way people are apparently taught these methods, there is also the fact (mentioned repeatedly on this blog) that: Fisher always denied, even with the lady tasting tea, that an “isolated record” of statistically significant results suffices: In relation to the test of significance, we may say that a phenomenon is experimentally demonstrable when we know how to conduct an experiment which will rarely fail to give us a statistically significant result.’ (Fisher 1935, p.14)It follows that, for Fisher, even showing the (statistical) reality of an experimental effect, much less showing the evidence of a specific explanation of the effect (be it an evolutionary story about beauty and daughters or something else), requires going beyond an isolated record.’


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