Affymetrix Exon Array Data Analysis (1/14/2015)

Tue, Jan 13, 2015 at 9:57 PM

Customer: My lab conducted microarray study using Affymetrix GeneChip® Exon 1.0 ST Array recently. The purpose of our study is to compare gene expression pattern between cells isolated from disease state Vs. that of adjacent normal tissue. We are looking for help in analyzing our microarray data (such as pathway analysis) to better understand our existing data. May I know which software programs do you use to conduct pathway analysis on data generated from high-throughput experiment?

Wed, Jan 14, 2015 at 8:24 AM

AccuraScience LB: Affymetrix's Expression Console can be used to perform basic processing of the exon array data, though often times we will use packages from the Bioconductor suite to perform additional analysis, e.g., rma package for quantile normalization (to remove/reduce chip-level bias and ensure the data from multiple chips are comparable), limma package for performing linear model-based differential expression analysis, and qvalue package to produce false discovery rate (FDR) for evaluating significantly differentially expressed genes. Following differential expression analysis, we would often invoke DAVID to perform pathway analysis, which will produce lists of significantly enriched biological pathways (denoted with gene ontology terms) among the up- and down-regulated genes. Other pathway definitions are possible - which we could discuss further if you would like.