Biological Data Analysis: Homework 9

Due Thursday, Dec. 1

You must type this and all other homework assignments. Do not e-mail the assignment to me; turn it in early (at 322 Wolf) for a foreseeable absence, or turn it in late after an unexpected absence from class.

Find a recent paper in your field of interest. If you are a grad student or an undergrad doing research in someone's lab, it should be a paper from your lab; if you're not in a lab, it can be anything that interests you. It can be one of the papers you used for homework 1 or homework 4, but it doesn't have to be. The paper must describe original experiments and results; it cannot be a review paper or theoretical paper.

Identify one experiment that is described in the paper and is analyzed using one of the statistical tests we've talked about this semester. Give the citation information for the paper (authors, year, article title, journal title, volume, pages) in any format you like. Write a couple of sentences describing the experiment in terms your classmates would understand, and say what statistical test the authors used. Also say how the authors presented the results of the experiment: a table, a graph, a P-value given in the text, etc.

Here's an example of what I'm looking for:

McDonald, J.H. 2013. Geographic variation in Megalorchestia californiana allele frequencies may be caused by winter rather than summer temperatures. Marine Ecology Progress Series 488: 201-207.

McDonald (2013) counted allele frequencies for the glucose-6-phosphate isomerase (Gpi) gene in the crustacean Megalorchestia californiana at multiple locations on the Pacific coast of the United States. He used simple logistic regression with January mean temperature at each location as the measurement variable and allele frequency as the nominal variable. He presented the results in a table showing the pseudo R2 and a graph of allele frequency vs. temperature. The graph did not have any error bars.

Next, find four other papers that do the same kind of experiment. Each set of papers should have different authors, so you will get papers from five different labs (including the first one). The easiest way to find more papers with the same kind of experiment will be to look at the Introduction and Discussion sections of the first paper, and see who they cite as doing the same kind of experiment. For the example, the discussion section of McDonald (2013) says "There have been numerous biochemical studies of Gpi polymorphisms with allele frequencies associated with temperature (Watt 1977, Hoffmann 1981, Watt 1983, Hall 1985, Zera 1987, Van Beneden & Powers 1989, Patarnello & Battaglia 1992, Dahlhoff & Rank 2000)," so those references would be a good place to look for other experiments that compare allele frequency and temperature. Note that the experiments just have to be the same kind of experiment, not exactly the same. For my example, I could look for papers correlating allele frequencies at other genes besides Gpi, with other measurement variables besides temperature.

Give the citation information and a short description of the experiment and statistical test for each of the papers you've found. It's possible that some of these papers will use a statistical test that we haven't talked about in class; that's okay.

Finally, write a few sentences about what you've learned. Did everyone use the same statistical test for similar experiments? Based on what you've learned this semester, does it seem like the best test to use? If different authors used different tests, did they seem to have good reasons for choosing different tests, or were some authors using the wrong test? Did everyone present their results the same way?

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