SSC 2009 Annual Meeting

2009 Annual Meeting of the SSC in Vancouver

Using Bioconductor for High Throughput Data

May 31, 2009
Vancouver, BC


Presenter: Robert Gentleman and members from his group at the Fred Hutchinson Cancer Research Center Herbold Computational Biology Program.

This workshop will be comprised of two different topics and participants will be required to bring their laptops with R and Bioconductor loaded on them (further details will be emailed to participants). Enrollment is limited for this hands-on workshop.

Morning Abstract

We will consider the two basic approaches used to find functional groupings of genes. One approach relies on the identification of differentially expressed genes followed by the use of Hypergeometric tests to identify over-representation of different groups. The second approach is called Gene Set Enrichment Analysis (GSEA) and it uses all genes (after some basic filtering) and regression-like analysis to identify predefined sets of genes whose members show a systematic variation from the expected behavior.

Afternoon Abstract

We will provide a brief introduction to data from ultra-high throughput sequencing technologies (Solexa, 454, Solid). Basics of quality assessment will be covered. An introduction to the identification of transcription factor binding sites (via ChIP-seq) will be given. Some basics of representation, interactions with genome browsers will also be covered.

About the Leader:

Robert Gentleman is well known as a co-developer, along with Ross Ihaka, of the R language and more recently for his new research project, Bioconductor. He is the Head of the Program in Computational Biology at the Fred Hutchinson Cancer Research Center in Seattle. His research interests are primarily in statistical computing.