Agilent Feature Extraction Software (v9.5) Reference Guide
This document is the official reference guide for Agilent Feature Extraction Software version 9.5. It explains default protocol settings for gene expression and CGH analyses, QC report interpretation, text and XML file outputs, and how algorithms calculate results. It also includes command-line integration instructions and technical acknowledgments for third-party software components.
The guide is structured into chapters covering protocol defaults, QC report results, parameter listings, algorithm explanations, and command-line usage. It is intended for users who need detailed technical information to interpret and use the software effectively.
This guide covers default protocol settings, QC report interpretation, text and XML file outputs, algorithm calculations, and command-line integration for Agilent Feature Extraction v9.5.
The guide includes protocols for 2-color gene expression, 1-color gene expression, CGH, and non-Agilent protocols.