we need people like him means that our journals are failing us. already published and someone like Keith—and I honestly don’t
The kinds of things that Keith spends time finding out—what did know of too many other people like Keith—does the reanalysis.”
[the researchers] actually do—that’s what methods and results are To address this time crunch faced by even the most diligent
supposed to be for in journals. … We have to figure out how to do reviewer, Baggerly and his colleagues have been making checklists
science without needing people like Keith.” for authors and reviewers that address the most common prob-
Some of the problems that Baggerly regularly encounters, those lems. “There are a whole bunch of really basic things, but we’re
barriers to reproducibility such as incomplete methods sections, are writing them down explicitly because those are the questions that
caused by the limited space in journals and could be resolved by we’re finding that we’re really needing to ask over and over and
publishing an expanded methods section online, for example. But over,” he said.
other problems are not so easily addressed. The high-throughput What is the number-one problem that he encounters?
microarray and proteomic studies that Baggerly analyzes are sub- Bookkeeping. “It’s not sexy, it’s not higher mathematics. It’s book-
stantially more complex than the typical single-gene or -protein keeping … keeping track of the labels and keeping track of what
study. These complex analyses require a multidisciplinary approach, goes where,” Baggerly said. “The thing that we have found repeat-
with researchers collaborating across fields and long distances. edly in our own analyses is that it actually is one of the most dif-
Unfortunately, few reviewers have the expertise to understand and ficult steps in performing some of these analyses.”
critically examine the validity of such a wide-ranging study in its Just a simple mistake such as mislabeling a cell line as sensitive to
entirety. “There is this tendency to say, ‘Well, I understand the a certain drug instead of resistant could have serious consequences.
analysis so the biology is probably OK,’ or ‘The biology sounds “I’m not really worried about particularly esoteric mathematics.
plausible so the analysis must be OK,’ ” Baggerly said. “In many Most of the stuff that I’m worried about is very clearly understand-
cases, the full steps of the analyses are rarely understood by one ing what was done at each of the steps involved.”
person. And as a result, a whole lot of confusion and ambiguity Baggerly hopes that others take his message seriously, but his influ-
can slip in.” ence is already apparent to some. “One thing I’ve learned [from him]
However, the reanalyses that Baggerly and his colleagues per- is to document, document, document every step of the analysis so
form require something that few reviewers or readers have: time. that I wouldn’t feel nervous if someone handed data that I had ana-
“To actually go into the detail that Keith does is not something that lyzed to Keith Baggerly. He may disagree with the analysis method I
the average reviewer has time to do,” McShane said. “So we’ve sort chose, but he can reproduce it,” McShane said.
of been forced into a situation where, unfortunately, if the results As Baggerly said, “Only if the data are reproducible can you talk
are artifacts and won’t hold up, we don’t find out until the paper’s about whether they’re right.” n
ASA / NCHS
Research Fellowship Program
“
bridge
the gap
The ASA, in cooperation with the National Center for Health Statistics
between (NCHS), created the ASA/NCHS Research Fellowship Program to bridge the
academic
gap between academic scholars and government health research programs. Fellows
work to solve methodological problems and study analytic issues relevant to
scholars
NCHS programs, data, and facilities. Applicants should have a recognized research
and
record and considerable expertise in the area of proposed research.
government
The application deadline is November 30, 2008,
health
for fullest consideration; however, applications will be accepted throughout the year
research
until positions are filled. For more information, visit www.amstat.org/nchs.
programs
”
20 AMSTAT NEWS OCTOBER 2008
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