Agilent GeneSpring GX Probe Summarization Guide

About this manual

The document describes the three key tasks of probe summarization algorithms: background correction, normalization, and probe summarization. It details how these steps are implemented in the RMA (Robust Multi-array Analysis) method used by Agilent GeneSpring GX software.

Specific instructions are provided for analyzing Affymetrix expression data using both GeneSpring GX 7.3.1 and GeneSpring GX 9.0. The guide covers importing data, selecting file formats and genomes, choosing preprocessing algorithms (RMA or GC RMA), adding sample attributes, and configuring probe summarization options.

What's inside

• Probe Summarization Algorithms
• Definition and Applications
• Analyzing Affymetrix Expression Data
• Importing Data
• Choosing File Format and Genome
• Selecting Preprocessor
• Sample Attributes Window
• Selecting ARR Files
• Probe Summarization Options

Specifications

Frequently asked questions

What is the RMA algorithm?

RMA (Robust Multi-array Analysis) is a method for normalizing and summarizing probe-level intensity measurements from Affymetrix Gene Chips.

Which preprocessing algorithms are available in GeneSpring GX?

Users can select the 'RMA' or 'GC RMA' preprocessing algorithm when importing data.