From CEL Files to Annotated Lists of Interesting Genes
One of the most popular applications of microarray technology is the identification of genes that are differentially expressed in two populations.With Affymetrix GeneChip technology, there are several steps between hybridization and the selection of interesting genes. The steps of preprocessing to improve signal to noise ratios, choosing a summary statistic for appropriate ranking of genes, and deciding on a final filter for candidate genes are largely statistical in nature. In this chapter, we demonstrate Bioconductor tools useful for creating such lists. We start from the raw probe level data (CEL files) and conclude with the creation of annotated reports.
KeywordsInteresting Gene Volcano Plot Average Fold Change Probe Level Data False Discovery Rate Adjustment
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