Using Our Discipline to Enhance Human Welfare
August 7 - 11, 2005
Analysis of Gene Expression Data Short Course, JSM2005
Terry Speed1,2, Jean Yang3,
Ben Bolstad2 and James Wettenhall1
Augst 6-7, 2005
1. Walter and Eliza Hall Institute of Medical Research
2. Department of Statistics, University of California, Berkeley
3. University of Sydney
Lecture Slides in PDF format (Annotation slides added Aug 22)
Each lab description lists the required software and data for that lab. An
overall list of software for the entire workshop is given in the following
section (Required Software).
- Lab 1. lab1.html
- Reading raw two-color microarray data into R, comparing the
performance of different image analysis software using diagnostic plots,
identifying control spots and blank spots on the arrays, and normalizing the
- Lab 2. lab2.html
- A continuation of the topics from lab 1, using a different data set.
- Lab 3. lab3.html
- Reading raw Affymetrix microarray data into R, assessing the quality
of the data using diagnostic plots, and normalizing the data.
- Lab 4. lab4.html
- Fitting linear models to microarray data, finding differentially
expressed genes, linking gene lists to external databases, using diagnostic
plots to assess the performance of the linear model, and using Venn diagrams
to find genes differentially expressed for more than one pair of conditions.
- Lab 5.
- Advanced Linear Modelling and Time-Series Analysis
- Lab 6. lab6.html
- Classification and clustering of microarray data.
- Lab 7. lab7.html
- Gene ontologies and gene sets. Finding statistically significant
over-represented (or under-represented) gene ontologies in a set of
differentially expressed genes compared to a reference list of genes.
Methods for determining whether a pre-defined set of genes is differentially
expressed in circumstances where it is difficult to measure whether individual
genes are differentially expressed.
As well as checking the overall list of required software, you may also wish
to check each individual lab sheet for a list of software required for that
Please check whether you already have the "Drosophila Embryo",
"Hyperdip" and "Estrogen" packages from the Required Software. (These data sets are stored within R packages.)
Past Microarary Workshops
Last modified: August 22, 2005