BISC 643, Biological Data Analysis, Fall 2014

Section 010

Tuesdays and Thursdays, 11 a.m.-12:15 p.m.

217 Gore Hall

Instructor: John McDonald
322 Wolf Hall (office)
E-mail: mcdonald@udel.edu
Phone: 831-2007 (I rarely check messages, so e-mail is better)
Class web page: http://udel.edu/~mcdonald/statsyllabus.html


Note: Homework assignments and exam study guides without links are not ready yet.

Date Day Lecture topic Homework due
Aug. 26 Tuesday Introduction;
Steps in analysis;
Kinds of biological variables
 
Aug. 28 Thursday Confounding variables;
Probability
 
Sept. 2 Tuesday Hypothesis testing and alternate schools of statistics ;
Exact test of goodness-of-fit
Homework 1
Sept. 4 Thursday Power analysis  
Sept. 9 Tuesday Chi-square test and
G-test of goodness-of-fit;
Using spreadsheets for statistics
Homework 2
Sept. 11 Thursday Chi-square test,
G-test
and Fisher's exact test of independence;
Graphs
 
Sept. 16 Tuesday Repeated tests of goodness-of-fit;
Cochran-Mantel-Haenszel test
Homework 3
Sept. 18 Thursday Descriptive statistics: Central tendency  
Sept. 23 Tuesday Descriptive statistics: dispersion,
standard error and
confidence limits
Homework 4
Sept. 27 Thursday One-sample and
two-sample t-tests;
Introduction to SAS
 
Sept. 30 Tuesday Parametric assumptions:
Normality;
Homoscedasticity;
Data transformations
Homework 5
Oct. 2 Thursday First exam; see the study guide and the answers  
Oct. 7 Tuesday One-way anova:
testing homogeneity of means
 
Oct. 9 Thursday One-way anova:
post-hoc tests and partitioning variance
 
Oct. 14 Tuesday Welch's anova;
Kruskal-Wallis test
Homework 6
Oct. 16 Thursday Nested anova  
Oct. 21 Tuesday Two-way anova;
Homework 7
Oct. 23 Thursday paired t-test;
Wilcoxon signed-rank test
 
Oct. 28 Tuesday Linear regression and correlation Homework 8
Oct. 30 Thursday Second exam (see the study guide and the answers)  
Nov. 4 Tuesday Election Day, no school!  
Nov. 6 Thursday Spearman rank correlation;
Polynomial regression
 
Nov. 11 Tuesday Analysis of covariance Homework 9
Nov. 13 Thursday Multiple linear regression  
Nov. 18 Tuesday Simple logistic regression,
Multiple logistic regression
Homework 10
Nov. 20 Thursday Multiple comparisons  
Nov. 25 Tuesday Meta-analysis Homework 11
Nov. 27 Thursday Thanksgiving, no school!  
Dec. 2 Tuesday Review for final exam Homework 12
December 11
10:30 a.m.-12:30 p.m.
Thursday Final exam See the study guide

Purpose of the course

This course is designed for biologists who want to apply appropriate statistical tests to their data, and who want to understand the statistical tests that other biologists have used. We will therefore spend little time on the mathematical basis of the statistical tests, focusing instead on how to choose the appropriate test for a given data set, how to design experiments to make them more suitable for statistical analysis, and how to interpret and present the results of statistical tests. While it would be impossible to cover every statistical test ever used by biologists in a single course, we will cover many of those techniques that are commonly used.

At the end of the course, you should be able to determine the correct statistical technique to apply to many biological experiments, and you should be able to apply each technique and interpret the results. You should also be able to recognize experimental designs for which you have not learned the appropriate statistical test, and you should be able to ask intelligent questions when consulting with a statistician about such experiments.

Office hours

There are no fixed office hours. You can make an appointment by talking to me before or after class or by e-mailing me. If you have questions while studying or doing the homework assignments, feel free to e-mail me or drop by my office.

Textbook

We will use an online textbook, Handbook of Biological Statistics. It is designed for online use, but if you want to print individual pages, they are formatted to print well (with most of the extra junk, like the sidebar and banner, omitted to save space). I am putting the finishing touches on the third edition, and once it's done, you'll be able to download a pdf of the entire book and print it yourself, or buy a bound copy for about $20. But until then, you'll be using drafts of each new chapter.

Attendance and lecture policies

Attendance is not mandatory, and you will not be graded on your in-class participation. However, I think it will be a lot easier to learn the material if you attend class. Homework assignments and exam study guides will be available from the class web page (http://udel.edu/~mcdonald/statsyllabus.html). If you are absent when a homework assignment is due, please try to turn in the assignment before the next class (you can slide it under my office door, 322 Wolf, if I'm not there). Do not e-mail me your homework assignments; I will not grade them. You must give me your homework assignments on paper.

I try to make the class as interactive as possible, as I find standard lectures to be rather boring. I will therefore call on each of you many times during the semester, whether or not you raise your hand. If this makes you uncomfortable, I can assure you that it would have terrified me when I was in college. Many students have reported on their evaluation forms that being forced to participate kept them attentive in the class and gave them good experience in speaking out. If you do not know the answer to a question, say "I don't know"; sometimes, that's the answer I'm looking for, and even if it's not, I'll try to go to someone else quickly.

I have found that the use of computers during class is distracting for both the students using them and those sitting nearby. You may not use laptops, tablets, smartphones, or other electronic devices during lectures. If I see you using such devices, I'll assume you're looking at porn and mock you accordingly.

Grading

Your grade will be based on the following:

15% First exam
25% Second exam
45% Final exam
15% Homework assignments

The grades will not be curved. The points from the homework and exams will be combined and converted to letter grades as follows:

A 93-100; A- 90-92.9; B+ 87-89.9; B 83-86.9; B- 80-82.9; C+ 77-79.9; C 73-76.9; C- 70-72.9; D+ 67-69.9; D 63-66.9; D- 60-62.9; F 0-59.9.

If you are less than 3 points below the minimum grade needed you need for your program (such as an undergraduate biology major with 67 to 69.9 points, or a biology grad student with 80 to 82.9 points), you will be given the opportunity to take an incomplete grade and complete an extra credit project. This project will be a lot of work, such as surveying the statistical tests used in a large set of scientific papers and critiquing their correctness. Upon satisfactory completion of the project, you'll get the minimum grade needed for your program (such as C- for undergraduate biology majors or a B for biology grad students). There will be no other extra credit.

Exams

The exams will be cumulative. The main emphasis of the exams will be testing your knowledge of what the appropriate statistical test is to use in a particular situation and how to interpret the results. You will not be allowed to use reference books or notes during the exams, and you will not need a calculator. If your native language is not English, you will be allowed to use a dictionary.

Homework assignments

A homework assignment is due on most Tuesdays. They will be available on the class web page a couple of weeks before they are due. I will not hand out printed copies of the assignments in class.

The homework assignments make up a relatively small portion of your grade, and they will be loosely graded; if you make a sincere effort on all parts of an assignment, you will probably get full credit. Despite this, I suggest that you put a lot of effort into the homework. Many of the skills I hope you learn from this class can only be learned by doing, not by listening to me talking, so your statistical education will be incomplete (and you will struggle on the exams) if you do not do the homework to the best of your ability. Please drop by my office or e-mail me if you need help on the homework.

Software

We are going to use spreadsheets for most of our data analysis. The web page for almost every statistical test will include a spreadsheet that you can download and use with the Windows or Macintosh versions of Excel. As a UD student, you can download Microsoft Office, which includes Excel, for free from UDeploy. The spreadsheets should also work with Calc, part of the free OpenOffice.org suite of programs.

I like using spreadsheets for statistics because most of you already know how to use them, and because they make it easy to combine graphics with the statistical tests. If you're interested in a field that only uses fairly basic statistics, such as molecular or cell biology, the tests that you can do with spreadsheets are likely to be all you'll ever need.

Wherever possible, I've linked to someone else's web page that will perform each statistical test, and you may use them for the homework if you prefer. I found most of these web pages using John Pezzullo's excellent list of Interactive Statistical Calculation Pages, which is a good place to look for information about tests that are not discussed in this course. For most tests, the web page version is not as easy to use as a spreadsheet, and many web pages only handle limited sample sizes. Some web pages, however, do tests that would be difficult to set up on a spreadsheet.

Each of my web pages about a statistical test will also include instructions for performing the statistical test using SAS. SAS is a powerful but user-unfriendly statistical package that can do statistical analyses that are far beyond the abilities of spreadsheets. While I don't expect you to become an expert in SAS, I'm going to try to teach you some of the basics this fall. Most of the homework assignments will require that you do each statistical test two ways, once with a spreadsheet or web page, then again with SAS. If you have problems with SAS, do not stay up all night struggling with it. Instead, send me an e-mail with as much information as possible (your SAS program, the error messages you're getting, a picture of your computer with smoke coming out of the back), and I'll try to help you. If there isn't time for me to respond before the homework is due, put this information in your homework assignment.

If you already know another comprehensive statistical program, such as R, SPSS, or Stata, you may use it on the homework assignments to check your answers. However, you will still be required to use spreadsheets and SAS for the homework. This is because I do not know anything about R, SPSS, Stata, etc. and can't help you with them.


Return to John McDonald's home page

This page was last revised October 20, 2014. Its URL is http://udel.edu/~mcdonald/statsyllabus.html