Biological Data Analysis:
Second exam study guide

This is the study guide for the second exam in Biological Data Analysis, fall 2009. The exam will be on Tuesday, October 20. You may not use your notes or textbook during the exam; if English is your second language, you may use a dictionary. You will not need a calculator.

The exam is cumulative; about a third of the questions will be about material covered in the first part of the semester. You should look at the first exam and the first study guide.

You should primarily study your lecture notes, the web pages on different topics (linked from the syllabus), and the homework assignments. In addition to the topics covered on the first exam, you should be familiar with:

• Statistics of central tendency (arithmetic mean, median, mode);
• Statistics of dispersion (range, variance, standard deviation, coefficient of variation);
• Standard error of the mean
• Confidence limits
• Student's t-test
• Model I vs. Model II one-way anova (if I describe a data set, you should be able to say which model is appropriate)
• Partitioning of variance components
• Planned comparisons
• Unplanned comparisons of pairs of means
• Gabriel's comparison intervals
• Tukey-Kramer method
• Assumptions of anova
• Bartlett's test of homogeneity of variances
• Data transformations
• Kruskal-Wallis test

The exam will consist of about 15 to 20 short-answer questions. Some of them will consist of me describing an experiment, then asking what statistical test is appropriate. If your answer is "one-way anova," you must specify model I or model II. If there are only two groups, you may say "one-way anova, model I" or "Student's t-test," as they are mathematically equivalent. Unless the question makes it clear that the data are non-normal, you should assume that the data meet the parametric assumptions (normality and homoscedasticity). Other questions will focus on the step-by-step approach to an anova; I may describe some of the steps in an experiment, then ask you what the next step is.

On this exam, I will not ask you to lisk the variables in an experiment and say whether they are measurement, nominal or ranked. That is a good way to help you decide on the appropriate statistical test, however.

Here are some example questions:

1. You have placed ten egg masses, each representing a separate family, of treehoppers on a host plant that they don't normally eat. After one month, you measure the body length of each treehopper. You are interested in whether there is genetic variation among the families in ability to grow on this host plant. What are two statistical tests you could use to test whether there is variation among the families in body length?
   How would you decide which was more appropriate?
2. You are interested in the effects of fertilizer on mitosis in onion root tips. In an onion root tip grown without fertilizer, you count 701 cells in interphase, 283 cells in prophase, 29 cells in metaphase, 56 cells in anaphase, and 100 cells in telophase. In an onion root tip grown with fertilizer, you count 942 cells in interphase, 576 cells in prophase, 97 cells in metaphase, 115 cells in anaphase, and 273 cells in telophase. What statistical test would you use to analyze these data?
3. You have measured the height of the arch of the foot in athletes from nine women's teams: soccer, basketball, rugby, swimming, softball, volleyball, lacrosse, crew and cross-country. Give a set of at least three orthogonal planned comparisons of the means from these sports.
4. You want to know whether the gene that codes for mannose-6-phosphate isomerase (MPI) is expressed differently in liver tumors than in normal livers. You take one biopsy from each of 27 normal livers and 32 cancerous livers and measure the amount of MPI mRNA in each one. Which test should you use?
5. Glacier-Waterton International Park is in Montana and Alberta. While backpacking through the park, you see 8 black bears and no grizzly bears in the Montana side of the park; after crossing the border into Canada, you see no black bears and 6 grizzly bears in the Alberta side of the park. You want to know whether there a difference between the two parts of the park in the proportion of bears that are grizzly bears. Which test should you use?
6. Because of the long tail feathers, male swallows mount the females from either the right or the left. You want to know whether they have a preference for one side, so you observe 17 pairs of mating swallows. Four males mount from the right side, while 13 mount from the left. Which test should you use?
7. You are planning to do experiments on chicken feed with different ratios of corn meal to soybean meal. To prepare for these experiments, you buy 20 bags of corn meal and 14 bags of soybean meal and put them in a cool, dry place. A few weeks later, when you finally decide to start mixing up chicken feed, you notice that 12 bags of corn meal have moth holes, while 2 bags of soybean meal have moth holes. You want to know whether moths prefer corn meal; which test should you use?
8. You are trying to see whether the genes Jam-1 and Pax-6 are genetically linked in zebrafish. You breed two individuals who are heterozygous for visible, dominant mutations at both genes, and you get 1600 offspring. If the two genes are unlinked, you'd expect 100 fish that were normal/normal, 300 that were normal at Jam-1 and mutant at Pax-6, 300 that were mutant at Jam-1 and normal at Pax-6, and 900 that were mutant/mutant. Which test should you use?
9. You want to breed miniature schnauzers that don't bark so much, by identifying those dogs that bark less than others to found the next generation. You obtain 30 miniature schnauzers, raise them under similar conditions, then record how many times each dog barks when a stranger approaches it. You do this five times for each dog. Which test should you use?
10. Two amphipod crustaceans live high on sandy beaches in Delaware, Talorchestia longicornis and Talorchestia megalophthalma. You want to know whether the proportion of each species is different on different beaches, so you collect about five hundred amphipods at Rehoboth Beach, Dewey Beach, Fenwick Island, and Cape Henlopen, and you count the number of individuals of each species at each beach. Which test should you use?
11. You want to know the effect of light source on pumpkins. You grow 10 pumpkin plants under natural sunlight, 10 pumpkin plants under fluorescent light, and 10 pumpkin plants under incandescent light. You remove excess flowers, so each plant will have only one pumpkin. After 3 months, you measure the diameter of the pumpkins. Which test should you use?
12. You want to know whether the presence of the malaria parasite (Plasmodium) in mosquitoes affects the West Nile virus. You collect 1200 mosquitoes. Half of them contain Plasmodium and one-third contain West Nile virus, so your null expectation is that one-sixth (200) of the mosquitoes will have both Plasmodium and West Nile virus. Instead, you find that only 148 mosquitoes have both. Which test should you use?
13. You want to know whether keeping sheep in indoor cages affects the weight of their offspring. You weigh 30 newborn lambs from ewes kept full-time in cages, 30 lambs from ewes caged at nights only, and 30 lambs from ewes kept outdoors. What should you do next?
14. You're planning a study of starfish size in different environments, in which you'll measure the length of arms of multiple starfish from each location. You're trying to decide whether to collect a large number of starfish and just measure one arm per starfish, or collect a smaller number and measure all five arms on each. You conduct a preliminary study in which you collect 27 starfish from one location and measure the length of each of the five arms on each starfish. Which test should you use?
15. You want to breed miniature schnauzers that don't bark so much, but you don't know whether there is any genetic variation for barkiness. You obtain 7 litters of miniature schnauzers, raise them under similar conditions, then record how many times each dog barks when a stranger approaches it. You do this once for each dog. Which test should you use?
16. You want to know whether mice can see colors. Twenty times a day for two weeks, you put a piece of mouse food in a small red box and put it in a cage with one mouse. The mouse can tip the box over and get the food out. At the same time, you also put mouse food in a green box; it looks and smells the same as the red box, but is glued shut so the mouse can't get the food out. At the end of the two weeks, you put the two boxes in with the mouse for 10 more times. The mouse pushes over the red box first eight times and the green box two times. Which test should you use?
17. When a click beetle is on its back, it rapidly flexes its body with an audible "click," flipping itself into the air and hopefully landing right-side-up. You want to know whether this flipping is random or whether the beetles tend to land on their feet. You catch a click beetle, put it on its back, and watch it click. You repeat this 12 times. The beetle lands on its feet 8 times and on its back 4 times. Which test should you use?
18. You have been observing a large troop of monkeys in the Philadelphia zoo. By careful observation of their social interactions, you have figured out the dominance heirarchy: which monkey is dominant over all, which monkey submits only to the most dominant, etc., all the way down to the poor monkey that submits to every other monkey. You want to know whether monkeys born at the Philadelphia zoo tend to be more dominant compared with monkeys brought from other zoos. Which test should you use?
19. You are studying the species diversity of algae in the highlands of Ecuador, and you want to know whether different taxonomic groups of algae are favored in different areas. In a pond at 400 meters elevation, you isolate 5 species of green algae and 3 species of cyanobacteria ("blue-green algae"); in a pond at 1500 meters, you isolate 6 species of green algae and 7 species of cyanobacteria. Which test should you use?
20. You want to know whether aspirin taken during pregnancy has an effect on the sex of offspring. You ask 1072 new mothers whether they took aspirin during the first three months of their pregnancy, and you also ask them whether they had a boy or a girl. Which test should you use?

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This page was last revised October 14, 2009. Its URL is http://udel.edu/~mcdonald/statstudy2.html