The goal of this class is to introduce statistical concepts and tools necessary to analyze gene expression array data. Advanced statistical material will be presented at an intuitive level. However, knowledge of basic hypothesis testing, ANOVA, linear and logistic regression are a prerequisite. 

TEXTBOOK 

The text for the course is "The analysis of gene expression data: Methods and Software". The companion website  has links to software packages described in the book.
 

SOFTWARE 

Students are free to use any software they like to analyze array data in this class. Some software packages will be illustrated in class, and occasionally live R analysis will be shown step by step. These link include a variety of free state-of-the art tools for array analysis. 

• Follow this Link to download the free statistical package R
• Bioconductor  software for bioinformatics, free, based on R companion website 
• A great crash course about R, by Bates and Lumley
• R packages for gene expression analysis
• The analysis of gene expression data: Methods and Software. Table of content of a forthcoming book and link to software sites
• A comprehensive survey of microarray data analysis software.  Link 

EXAMS

• Midterm 
• Final 

INSTRUCTOR

The instructor for this class is Giovanni Parmigiani. He is available via email at gp@jhu.edu, after class every Wednesday until 1pm, and by appointment.
 

RELATED LINKS

The web site of the microarray working group "Hopkins Expressionists", with links to software and papers by Hopkins faculty. 

A description of and information for the course "Introduction to Bioinformatics" M.E:440.714