Biological Data Analysis:
Second exam study guide
This is the study guide for the second exam in Biological Data Analysis,
fall 2012. The exam will be on Tuesday, October 23. 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.
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
- Statistics of central tendency (arithmetic
mean, median, mode);
- Statistics of dispersion (range, variance,
- Standard error of the
- 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
- Planned comparisons
- Unplanned comparisons of pairs of means
- Tukey-Kramer method
- Assumptions of anova
- 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.
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.
some example questions:
- You have placed ten egg masses, each
representing a separate family, of treehoppers on a host plant that they
don't normally eat. One month after the eggs hatch, 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. Which test should you use to determine how much variation there is among
the families in body length?
- 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?
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.
- 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?
- How could you make the preceeding experiment (on livers) less senstive to possible deviations from the assumptions of the test?
- 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?
- 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?
- 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?
- 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
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?
- Miniature schnauzer dogs are cute, but they bark 50 to 100 times every time they see a stranger. 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?
- 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?
- 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?
- 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?
- 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?
- 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?
- 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?
- 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?
- 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?
- 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?
- 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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