Multivariate Statistics in Ecology and Quantitative Genetics SS 2010
Lecture with Exercises (Vorlesung mit Übung): (3 Credit Points)
Instructors
Prof. Dr. Dirk Metzler and Dr. Martin Hutzenthaler
Time and rooms
May 17 2010 until June 4 2010
Lecture: Each day from 9:15 to
10:45 in room D00.013
Exercises: Each Monday from 11:15 to 12:00 in computer room C00.005
Each Tuesday - Friday from 16:15 to 17:45 in computer room C00.005
Please note: If you fully attend the course (which is required to get
the 3 ECTS points) you will need the time between the 11 a.m. and 4 p.m. to
solve exercises which will be given in the morning lectures and discussed in the
afternoon courses.
Requirements
Basic knowledge of statistics. If you are not already familiar with the
free R software, it may be a good idea
to install it on your computer and get a bit familiar with it before the
course starts. Some
examples (data
file FinchesSulloway.txt), R
tutorial, Martin's introductory R course.
Contents
In the exercises you will practice to analyse data with the methods listed below using the R software. We will discuss the interpretations of
the results and problems that may arise during the analysis. In the lectures we will explain the theoretical concepts behind the methods and show how these methods can be applied.
If you would like to discuss analyses of your own
datasets during the course, please contact D. Metzler or M. Hutzenthaler as soon as possible.
- Fundamental methods: Multivariate linear regression, Model
Selection, Analysis of Variance (ANOVA), Experimental
designs (nested, balanced, unbalanced,...), Graphical Inspection
of Fitted Models, Generalized Linear Models (GLM), Mixed
Effects Models
R-package: lme4
- Special Methods for complex ecological datasets:
ANCOVA,
Redundancy Analysis, Principal Component Analysis (PCA), Canonical
Correspondence Analysis,....
R-package: vegan
(see also
the ecology
task view)
- Analysis of Gene Expression Data (Microarray
data).
Multiple-Testing Problems, Variance-Stabilizing
Normalization, Regularization, reconciliation with gene ontologies (GO)...
R-packages: vsn,
limma,
multtest,
GOstats
- Special
Methods in Genetics: Mapping Quantitative Traits Loci (QTLs).
Keywords:
Haley-Knott regression, Composite Interval Mapping, Multiple-QTL
models,...
R-package: qtl
(see also
the genetics task
view)
Language: English
Course material
-
ANOVA: slides, R-script,
data files: clotting.txt,
chlorpheniraminmaleat.txt
-
more about
ANOVA: slides, exercises
sheet 1, R-script, abcdx.txt, transform.txt, CCRT.txt, SimpleCCRT.txt
-
Linear Models: slides, exercise
sheet 2, bp.txt
-
Generalized Linear Models: slides,
exercise sheet 3,
FinchesSulloway.txt,
TbDeerAndBoar.txt
-
Principal Component Analysis (PCA): slides, exercise
sheet 5, HeightShoeWeight.txt, EWU.txt
-
Redundancy Analysis (RDA): slides,
R-script,
exercise sheet 6,
exercise sheet 7,
artificialFishes.txt, RIKZGroups.txt
-
Correspondence Analysis (CA): slides,
R-script,
MexicanPlants.txt
-
Canonical Correspondence Analysis (CCA): slides,
R-script,
exercise sheet 8,
MexicanPlants.txt
-
Mixed-effects models slides, exercise sheet 9
-
QTL Mapping slides, R-script
-
Summary slides, exercise
sheet 10
Literature
-
Introductory statistics with R / Peter Dalgaard (Springer 2002)
-
Biometry: The Principles and Practice of Statistics in
Biological Research (3rd Ed.) / Sokal, Rohlf, (Palgrave Macmillan 1995)
-
Mixed effects models and extensions in ecology with R /
Alain F. Zuur, Elena N. Ieno, N. J. Walker,
Anatoly A. Saveliev, Graham M. Smith.
(Springer 2009)
-
Modern applied statistics with S / W. N. Venables ; B. D. Ripley. - 4.
ed. (Springer 2002)
-
A Guide to QTL Mapping with R/qtl /
Karl W. Broman & Saunak Sen (Springer 2009)
-
Analysing ecological data / Alain F. Zuur ; Elena N. Ieno ; Graham M.
Smith. (Springer 2007)
-
Genetics and analysis of quantitative traits / Michael Lynch ; Bruce
Walsh. (Sinauer 1998)
-
Introduction to quantitative genetics / D. S. Falconer and Trudy F. C.
Mackay. - 4. ed. (Pearson 1996)
-
Numerical ecology / Legendre & Legendre (Elsevier 1998)
-
Statistical Genetics of Quantitative Traits / Wu, Ma & Casella. (Springer 2007)
-
Bioinformatics and Computational Biology Solutions Using R and Bioconductor /
R. Gentleman, V.J. Carey, W. Huber, R.A. Irizarry, S. Dudoit (Eds.). (Springer
2005)
-
Mixed effects models in S and S-PLUS / Jose C. Pinheiro ; Douglas M.
Bates. (Springer, 2004)
Announcement in official LMU course overview
Last update: Dirk Metzler, June 3, 2010