Biological Data Analysis:Second exam study guide

This is the study guide for the second exam in Biological Data Analysis, fall 2015. The exam will be on Thursday, Nov. 5. 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; several 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:

• One-way anova
• Welch's anova
• Partitioning of variance components
• Tukey-Kramer method
• Assumptions of anova
• Kruskal-Wallis test
• Nested anova
• Two-way anova with replication
• Two-way anova without replication
• Paired t-test
• Wilcoxon's signed rank test
• Linear regression and correlation

The exam will consist of about 15 to 20 short-answer questions. Most of them will consist of me describing an experiment, then asking what statistical test is appropriate. Don't just say "anova," you must specify one-way, Welch's, two-way with replication, two-way without replication, or nested. Note that you can't just say "two-way anova," you must specify with or without replication. Don't just say "t-test," you must specify one-sample t-test, two-sample t-test, or paired t-test. If there are only two groups, you may say "one-way anova" or "two-sample t-test," as they are mathematically equivalent. You may say "two-way anova, without replication" instead of paired t-test. Unless the question makes it very clear that the data are non-normal or heteroscedastic, you should assume that the data meet the parametric assumptions (normality and homoscedasticity).

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 several eggs, of treehoppers on rose bushes, ten egg masses on azalea bushes, and ten egg masses on hydrangea bushes. You want to know whether treehoppers grow to different sizes on the different host plants. One month after the eggs hatch, you measure the body length of each treehopper. Which test should you use?
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 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 17 normal livers and 32 cancerous livers and measure the amount of MPI mRNA in each one. Which test should you use?
4. How could you make the preceeding experiment (on livers) less senstive to possible deviations from the assumptions of the test?
5. Glacier-Waterton International Park is in Montana and Alberta. You want to know whether Montana bears are different in size from Alberta bears. You capture 17 black bears and 24 grizzly bears in Montana, and 26 black bears and 11 grizzly bears in Alberta, and measure their weight. Which test should you use?
6. Because of the female's long tail feathers, male swallows mount the females from either the right or the left. You want to know whether they prefer to mount on the side that has the shorter tail feather, so you observe 17 pairs of mating swallows and measure the length of the female tail feather on the mounted side and the unmounted side. 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 want to test the effects of anabolic steroids on the muscle strength of elderly people. You put 150 old people on steroids, 200 old people on placebo, and 350 old people on no treatment. After one month, you measure the arm strength of each person. The standard deviation of arm strength for people on steroids is much higher than for the other two groups. Which test should you use?
9. 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?
10. Miniature schnauzer dogs are cute, but they bark 50 to 100 times every time someone comes to the door. You want to know whether they bark more when someone knocks on the door, or rings the doorbell. You go to the home of Otto the miniature schnauzer, ring the doorbell, and count the number of times Otto barks. You ring the doorbell and count the barks 5 times at Otto's house, and you also knock on the door and count the barks 5 times at Otto's house. You do the same think at the houses of Fritz, Hans, Rudolf, and Bob. Which test should you use?
11. You are planning a big study on hopping ability in people who've injured their anterior cruciate ligament, and you want to know whether you're going to have to control for height when comparing hopping distance. You get 34 volunteers, measure their height, and measure how far they can hop on one leg. What test should you use?
12. 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 go to Rehoboth Beach, Dewey Beach, Fenwick Island, and Cape Henlopen, collect about 500 amphipods from each beach, and count the number of individuals of each species at each beach. Which test should you use?
13. 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. When the pumpkins are three months old, you measure the diameter of the pumpkins. Which test should you use?
14. 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?
15. 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?
16. You want to breed miniature schnauzers that don't bark so much, but you don't know whether there is any genetic variation among families 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?
17. 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?
18. William the Wildlife Biologist wants to know whether the number of polar bears in Alaska has been decreasing. He has data for the total number of polar bears in Alaska, collected once each year for the past 30 years. He plots a graph with the year on the X-axis and the total number of polar bears on the Y axis and analyzes the data with linear regression/correlation. What makes William's choice of technique incorrect?
19. 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. If it lands on its back, it flips itself into the air again. You want to know whether the second flip is different in height than the first one. You collect 100 click beetles, put each one on its back, and record how high it flips. There are 52 beetles that land on their back and flip again, and you record the height of these second flips. You notice that the differences between the first and second flip are highly non-normal. Which test should you use?
20. You have been observing a large troop of monkeys in the Philadelphia zoo. Some of the monkeys were born there, and the other monkeys were brought there from other zoos. By careful observation of their social interactions, you have put the monkeys in order from most dominant to least dominant: 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?
21. 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?