BIOLOGY 446

STATISTICS FOR BIOLOGISTS (FALL 2014)

Dr. Joshua Plotkin

Office Hours: Thursday, 3:30p-4:30p, Lynch Labs room 219

TA's: Alexandra Brown (alexabr@sas.upenn.edu), Christel Chehoud (cchehoud@upenn.edu)

Mitchell Johnson (mitj@sas.upenn.edu), and Yang Ding (dingyang@sas.upenn.edu)
TA Email group: biology-ta-446@groups.sas.upenn.edu
Office Hours: TBA

Textbook
There is no textbook for this course, and you are not advised to buy any textbook. However,
Sternstein: Statistics. Barron's EZ series, Second Edition is available in the Penn bookstore, and page
references to Sternstein are listed in the syllabus below; references in parentheses imply that the
approach is rather different than that taken in class. However it should be noted that Sternstein is
often misleading and obscure, so that all material necessary for the course is given in class. Also,
substantial amounts of material given in class is not to be found in Sternstein.

Computing
The course does not focus on computers and statistical packages. However, any student may use a
statistical package in those homework questions involving computations, if he/she so wishes.

Website
Weekly homeworks and other material will be available through Penn’s blackboard site.

Assessment in this course consists of (i) marks in weekly homeworks, (ii) a mid-term exam, and (iii)
a final exam. These will contribute approximately 25%, 25% and 50% towards the final grade.

Homeworks are handed out each week, and are to be handed in the following week. They will graded
and discussed in recitation sessions within days of being handed in.

Exams. The tentative time and date for the mid-term exam is 12:00pm - 1:20pm, Thursday October
16. The final exam will be Monday December 15th, 12:00 pm - 2:00 pm.. Both the mid-term and the
final will be held in Leidy Labs room 10 with overflow seating in other rooms to be announced.

Recitations
Each week, four recitation classes are held in which homeworks and problems arising in lectures are
discussed. Each student should go to only one recitation class in each week. However, he/she may
choose, each week, to attend whichever recitation class is most convenient in that week. The times of
these recitations will be organized during the second week of the semester.

Academic Integrity
Students should be aware of Penn’s Code of Academic Integrity as summarized here:
http://www.upenn.edu/academicintegrity/. Students should write down their homework solutions
entirely on their own. Cases of misconduct will be referred to Penn’s Office of Student Conduct.

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COURSE OUTLINE Page references in Sternstein

0. Introduction

1. Probability theory

1.1 Discrete random variables and their probability

distributions. Parameters. (47)

1.2 Examples of discrete probability distributions.

1.2.1 Some numerically-defined distributions.

1.2.2 The uniform distribution.

1.2.3 The binomial distribution. 43-46, 57-57, 61-63

1.2.4 Other discrete distributions.

1.3 Concepts of mean and variance.

1.3.1 Definition of the mean. 49-50

1.3.2 Means for above distributions.

1.3.2.1 Numerically-defined distributions

1.3.2.2 Uniform
53, 58

1.3.3 Definition of the variance. 51 - 52

1.3.4 Variances of above distributions.

1.3.4.1 Numerically-defined distributions

1.3.4.2 Uniform distribution
54, 58

1.3.5 The "two-standard-deviation rule".

1.4 Continuous random variables.

1.4.1 Definition.

1.4.2 Mean and variance.

1.4.3 The normal distribution. 68-77

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 1.4.4 The normal approximation to
78-83

1.5 Many random variables.

1.5.1 Introduction.

1.5.2 Averages, sums and their properties.

1.5.3 Central Limit Theory

1.5.4 Binomial random variables as sums.

1.5.5 Properties of differences of random variables

1.5.6 Further comments on continuity correction

1.6 More on “data”.

2. Statistics

2.2 Estimation.

2.2.1 Estimation of the mean.

2.2.2 Estimation of the variance.

2.2.3 Confidence intervals

for the mean. (136 - 139)

2.2.4 Estimation of, and confidence interval for, the binomial

probability . (100 - 104)

2.2.5 Estimation in regression. 199 - 202

2.3 Hypothesis testing.

2.3.1 Introduction.

2.3.2 Informal example of hypothesis testing,

using the binomial distribution.

2.3.3 General principles and format

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 for a test of hypothesis. 143 - 151

2.3.4 Testing a hypothesis about a single

binomial parameter. 107 - 108

2.3.5 Testing for the equality of two binomial

parameters. 121 - 123

2.3.6 Contingency tables.

2.3.7 Larger contingency tables

168 - 173

2.3.9 Tests for means.

2.3.9.2 Normal theory tests, variance

(155 – 156)

2.3.9.3 Non-parametric tests

Rank-sum test (two populations)

Permutation procedures

2.3.10 Hypothesis testing in regression

2.4 Odd and Ends

2.4.1 Fisher’s Exact test, as a permutation test

2.4.2 Multiple Hypothesis testing

2.4.3 Fisher’s combined test