Statistics and Quantitative Biology Course

Gulbenkian Ph.D. Programme in Interdisciplinary Biology (PIBS)
Instituto Gulbenkian de Ciencia, Oeiras, Portugal
September 27-October 8, 2010

Lecturers

Jorge Carneiro Bio
Instituto Gulbenkian de Ciencia, Oeiras, Portugal

Programme

Monday, September 27

10h00-10h45 Overview

11h00-13h00 Stochastic processes, probability, and the central limit theorem
. . . . . . . . . . . (download pdf)

14h30-17h00 First steps in R
. . . . . . . . . . . (download pdf , data set)

Tuesday, September 28

10h00-12h00 R practice

14h30-15h30 Data exploration and representation: Informal data analysis

. . . . . . . . . . . (download pdf)

16h00-17h00 Describing data: Proportion, location, and spread

. . . . . . . . . . . (download pdf)

17h00-18h00 R practice

. . . . . . . . . . . (download pdf)

Wednesday, September 29

10h00-12h00 Uncertainty and uncertainty propagation
. . . . . . . . . . . (download pdf and R file)

14h00-17h00 R practice

Thursday, September 30

10h00-12h00 Hypothesis testing
. . . . . . . . . . . (download pdf)

14h00-17h00 R practice and Hypothesis testing assignments

Friday, October 1

10h00-17h00 Hypothesis testing assignments
. . . . . . . . . . . Leonor Mark (t-test)
. . . . . . . . . . . Jorge Jordi (Wilcoxon-Mann-Whitney)
. . . . . . . . . . . Ewa Claudia (ANOVA)
. . . . . . . . . . . Madalena Pedro (Fisher exact test of independence)
. . . . . . . . . . . Aybuke Krzysztof (Chi2 test of independence and homogeneity)

Monday, October 4

10h00-12h00 Hypothesis testing assignment reports and discussion
. . . . . . . . . . . Leonor Mark (t-test)
. . . . . . . . . . . Jorge Jordi (Wilcoxon-Mann-Whitney) pdf
. . . . . . . . . . . Ewa Claudia (ANOVA) pdf
. . . . . . . . . . . Madalena Pedro (Fisher exact test of independence) pdf
. . . . . . . . . . . Aybuke Krzysztof (Chi2 test of independence and homogeneity)

14h00-17h00 R practice
. . . . . . . . . . . (download data sets zip)

Tuesday, October 5

10h00-12h00 Relation between two variables: association, correlation, and regression
. . . . . . . . . . . (download pdf)

14h00-17h00 R practice
. . . . . . . . . . . (download data sets zip)

Wednesday, October 6

10h00-12h00 Multivariate analysis, PCA, and multidimensional scaling
. . . . . . . . . . . (download pdf)
. . . . . . . . . . . (download Krzysztof presentation on SVM)

14h00-17h00 R practice
. . . . . . . . . . . (download data sets zip)

Thursday, October 7

10h00-12h00 Linear and nonlinear models
. . . . . . . . . . . (download pdf)

14h00-17h00 R practice
. . . . . . . . . . . (download data sets zip and practical problem pdf)

Friday, October 8

10h00-12h00 Journal Club
. . . . . . . . . . . Leonor Mark pdf
. . . . . . . . . . . Jorge Jordi pdf

14h00-17h00 Journal Club
. . . . . . . . . . . Ewa Claudia pdf
. . . . . . . . . . . Aybuke Madalena Krzysztof pdf

Bibliography

Locations

Theoretical classes will be held at the Democritus auditorium above the cantine.

Practical classes will be held at the computer room under the library.

Software

The practicals of the course will be based on the R software. R is a powerfull free open-source software for statistical computing and graphics. It runs in any platform (Linux, MacOSX, or Windows).

R is available at http://www.r-project.org/

We encourage students to bring and use their own laptops during the practical classes, but desktop computers will be available in the practice classroom for everyone if necessary.

Please make sure that R software is properly installed in your laptop before the practical classes.