MGC MicroArray Analysis course June 2011
Introduction
Dear students of the MGC course on MicroArray Analysis,
On this webpage you can find all information related to the course:
the programme,pdf files of the presentations,
software and data needed in the practical sessions
of the course.
Presentations in PDF format
- Day 1
- Short introduction to datasets and tools ,
Judith Boer:
01.Introduction.pdf
- Experimental Design: Think before you start ,
Judith Boer:
02.Think.pdf
- Preprocessing and quality control ,
Hinrich Göhlmann:
03.Preprocessing and quality control.pdf
- Normalization ,
Judith Boer:
04.Normalization.pdf
- Introduction to R and Bioconductor , Judith Boer:
05.R.pdf
- Day 2
- Finding differentially expressed genes,
Renée de Menezes:
06.Differentially_expressed_genes.pdf
- Hierarchical and K-means clustering,
Marcel Reinders:
07.Clustering and PCA.pdf
- Cluster validation and principal component analysis,
Marcel Reinders:
08.Cluster Validation.pdf
- Day 3
- Classification and PAM ,
Paul Eilers:
10.Classification and PAM.pdf
- Testing groups of genes , Jelle Goeman:
11.Testing_groups_of_genes.pdf
- Day 4
- Power and sample size estimation ,
Maarten van Iterson:
12.Power and Sample size estimation
- Gene expression profiling; from computer to bedside,
Monique den Boer:
13.Interpretation_of_gene_list.pdf
- Day 5
- Interpretation of gene lists ,
Kristina Hettne and Herman van Haagen:
16.Interpretations of gene lists
- Databases and pathway analysis ,
Andrew Stubbs:
17.Databases and Pathway Analysis.pdf
- Presentation Cytoscape ,
Peter van Baarlen:
18.Cytoscape
Software
R and BioConductor are open source software. Information on downloading R and getting started can be found
here. Packages used in the course you can download here
Spotfire runs on a Crosslinks server in Rotterdam. Crosslinks-IT is a spin-off company from Erasmus MC, Department of Bioinformatics. Spotfire licenses can me requested at Crosslinks-IT
Anni2.1 is a webtool which is freely available from the Biosemantics Group Rotterdam-Leiden
DAVID is a webtool wich is also freely available from the DAVID website.
Cytoscape is a webtool wich is freely available from the Cytocape website.
If you use Excel to open your input or output.txt files, make sure the regional and language settings of your computer are set to international (US or UK).
Practical sessions data
Instructions and data files for the course practicals are available as zip-files.
Day 1
Choose the type of data according to your own experiments or plans:
Normalization and quality control in R using platform comparison study Affymetrix data
Normalization and quality control in R using platform comparison study, Illumina data
Normalization and quality control in R using platform comparison study, Agilent two-color-data
Extra: Finding differentially expressed genes in R using platform comparison study, Affymetrix, Illumina and Agilent data
Day 2
Finding differentially expressed genes in R using DMD data
Clustering in Spotfire
Extra: Introduction to Spotfire
Day 3
Classification in pamr using ALL data
Testing groups of genes in R using DMD data
Day 4
Power: instructions and R package SSPA
Data analysis of ALL samples
Day 5
Interpretation of gene lists
Cytoscape
Spotfire Logon
When you start the Spotfire client after you login, it will give you the
Spotfire Server login screen. Here you have to login into the Spotfire
application. After the course, the account will be inactive.
Server = http://spotfire-decisionsite.erasmusmc.nl/
Username = sf_course
Password = welcome
