STA 290 Seminar: Sandrine Dudoit (UC Berkeley)

Statistics Seminar: STA 290

Thursday, November 10th, 2011 at 4.10pm, MSB 1147 (Colloquium Room)

Refreshments: 3.30pm, MSB 4110 (Statistics Lounge)

Speaker:   Sandrine Dudoit (Dept Statistics/Graduate Group in Biostatistics, UC Berkeley)

Title:       Normalization and Differential Expression in RNA-Seq

Abstract:
This talk concerns statistical methods and software for the analysis of RNA
abundance by sequencing (RNA-Seq). We first present exploratory data analysis
(EDA) approaches for quality assessment/control (QA/QC) of RNA-Seq reads. Next, we propose within-lane normalization methods to adjust for sample-specific
gene-level effects such as length and GC-content. We also provide between-lane
normalization procedures to account for distributional differences such as
sequencing depth. Finally, we consider the quantitation of (differential) gene
expression levels using generalized linear models (GLM). This work was
motivated by a collaboration with the Sherlock Lab on transcriptome analysis in
Saccharomyces. Our exploratory data analysis and normalization methods are
implemented in the open-source Bioconductor R package EDASeq (http://www.bioconductor.org).