Analysis of microarray gene expression data using R/BioC and web tools

General info

Date: 20 Jun 2011 - 24 Jun 2011
Location: Erasmus MC, Rotterdam
Website: http://www.molmed.nl/
Contact(s): Frank van Vliet

Description

The course is intensive, and covers the basic concepts and methods required for microarray expression analysis. Presentations are followed by hands-on computer sessions to directly apply and get more insight in the analysis methods. One afternoon is dedicated to the analysis of a new data set, allowing the students to refresh and extend their analysis skill. After the course, the Presentations, practicals and test data will remain available for future reference. Software packages used are mostly freeware, including the statistical software R, Bioconductor, Cytoscape and web tools. The only commercial tool used is Spotfire.

The participant has insight in the issues involved in good experimental design, including power to detect differential expression.
The participant knows and can perform analysis steps in microarray data analysis, visually present and judge the results for:
• quality control and preprocessing,
• finding differentially expressed genes,
• cluster analysis,
• classification analysis,
• pathway testing.
The participant has insight in the different algorithms and options available to perform an analysis, and can make an informed choice.
The participant knows the pitfalls of existing analyses and is able to critically judge the statistical analysis of microarray expression data performed by others.

Teachers:

Judith Boer, Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam and Center for Human and Clinical Genetics, Leiden University Medical Center
Andrew Stubbs and Elizabeth McClellan, Department of Bioinformatics, Erasmus MC, Rotterdam
Paul Eilers & Dimitris Rizopoulos, Dept. of Biostatistics, Erasmus MC, Rotterdam
Johan de Rooi, Department of Bioinformatics and Department of Biostatistics, Erasmus MC, Rotterdam
Kristina Hettne/Jan Kors (t.b.d.), Biosemantics Group, Erasmus MC, Rotterdam
Monique den Boer & Leila Mohammadi Khankahdani, Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam
Maarten van Iterson, Center for Human and Clinical Genetics, Leiden University Medical Center
Jelle Goeman and Ramin Monajemi, Dept. Medical Statistics and Bioinformatics, Leiden University Medical Center
Renée de Menezes, Department of Epidemiology and Biostatistics, VUmc, Amsterdam
Hinrich Göhlmann, Bioinformatics Team of Johnson & Johnson Pharmaceutical Research & Development, a division of Janssen, Beerse, Belgium
Marcel Reinders, Information and Communication Theory Group, TU Delft
Peter van Baarlen, Guido Hooiveld, Mark Boekschoten , Wageningen University
Software: Dr. Mirjam van den Hout-van Vroonhoven, Department of Bioinformatics, Erasmus MC