This guide covers experimental design, statistical algorithms, and biological interpretation for analyzing Affymetrix GeneChip expression profiling data.
This document provides an overview of strategies for designing GeneChip® expression profiling experiments to generate high-quality results. It details how to mitigate technical and biological variance during sample preparation and outlines the use of software tools like GCOS for data management.
The guide further explains first-order data analysis, including quality assessment of .dat images and scaling strategies. It covers statistical algorithms used in single array and comparison analyses, as well as multivariate statistics for interpreting gene expression changes.
Acceptable A 260/280 ratios fall in the range of 1.8 to 2.1.
Ratios below 1.8 indicate possible protein contamination.