The CNIO Bioinformatics Unit, in collaboration with the Genomics Unit, organize an internal introductory course on microarray gene expression analysis, to be held on Wednesday, October 8th 2008, at the CNIO Seminars Room, 3rd floor.

This introductory course is targeted to researchers without previous knowledge on this field. We will cover the basic steps that should be followed to obtain a list of differentially expressed genes starting from raw microarray expression data.

The theoretical part of the course will be comprehensive and the similarities and differences between one- and two-color arrays will be discussed. For the practical part, an already published public dataset of Agilent two-color arrays will be used.

Students will get familiar with the raw data format, the background subtraction methods and the normalization procedures that are commonly used in differential expression analysis. Some notions on experimental design and statistical tests will be given, and attendees will learn the value of biological replicates and the importance of multiple testing corrections.

Finally, we will present some useful tools to visualize the results and review the clustering methods, making emphasis on the interpretation of the results.

The course is limited to 15 persons. Several laptop computers are available for the attendants, but they are free to bring their own laptops. Please contact us ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) in advance if you wish to attend the course.

Teachers

• Gonzalo Gómez and Daniel Rico, Bioinformatics Unit (CNIO)
• Orlando Domínguez, Genomics Unit (CNIO)

Course Agenda

• 09:00 Microarray platforms and procedures at CNIO Genomics Unit 
• 10:00 Raw data, microarray DBs and background correction (Theory: Raw Data, Background)
• 11:15 Coffee Break
• 11:45 Normalization and preprocessing (Theory) (Training: Slides, .xls file)
• 13:00 Lunch 
• 14:30 Differential expression analysis (Theory) (Training: Slides, .xls file)
• 16:00 Coffee Break 
• 16:15 Visualization and Clustering (Theory) (Training, .gct file)
• 17:00 Finish

Course Raw Data Files

• Zheng et al. Nat. Med. (2008)  (Article) (Suppl. Material)
  
• GEO Dataset: GSE10010
• Description File