This manual describes the functions and use of Agilent Genomic Workbench 6.5 Feature Extraction 10.10 software.
This document serves as a Reference Guide for the Agilent Genomic Workbench 6.5 Feature Extraction 10.10 software. It provides detailed descriptions of protocols available for use with the software, including default parameter values and results for various analyses such as gene expression (2-color and 1-color), CGH, ChIP, and miRNA experiments.
The guide explains how the Feature Extraction algorithms calculate results to help users interpret their data. It includes tables listing default settings for shipped and non-Agilent protocols, instructions on reading QC Reports, a listing of parameters in generated text files (FEPARAMS) and MAGE-ML XML files, and equations with sample calculations for the feature extraction process.
The guide covers gene expression (2-color and 1-color), CGH, ChIP, and miRNA experiments.
The software produces text files containing parameters and results, as well as MAGE-ML XML files.