Gene expression analysis using Affymetrix Microarrays
Overview
This course aims to illustrate the end to end workflow typically followed for analysis of Microarray based Gene Expression data. Although focuses on Affymetrix microarray data analysis, the steps can be applied to any other microarray platforms. The course starts with an introduction to microarray techniques and various platforms available followed by explanations on various databases and file formats and raw data structures. Next, we describe ExpressionSets, bioconductor object where raw data would be stored. This is followed by detailed explanation on quality assessment, pre-processing and normalization steps. Next, we move on to differential expression study with multivariate methods such as PCA, MDS, Clustering. Last we talk on Gene set enrichment analysis, Pathway enrichment analysis. Overall, you will be introduced to deep statistical concepts, advanced visualization methods and many bioconductor packages.
Course content
Introduction
Databases
Raw data and File formats
Data structure
Quality assessment
Data pre-processing
Relative Log Expression (RLE) data quality analysis
Data Filteration
Probe annotation Differential expression
Clustering and classification Visualization
Pathway enrichment analysis Duration
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