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Manual

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EASI Database Users Manual

Data Analysis Fundamentals Manual  The purpose of this manual is to provide users with a comprehensive description of different terms used in GeneChip® expression analysis, to present users with information on assessing sample and array quality, and to supply instructions on how to use the Affymetrix® Microarray Suite (MAS) software to analyze expression data.

Data Mining Tool 3.0 Manual  A user guide to Affymetrix® Data Mining Tool (DMT) software that can filter, query, and analyze published databases of GeneChip® spotted array expression data.

Expression Analysis Technical Manual  This manual is a technical guide for using GeneChip expression analysis probe arrays and includes a series of protocols on RNA isolation, fragmentation, labeling, and all steps necessary to go from total RNA to hybridization on a GeneChip array and initial analysis. It also includes protocols on cleaning and maintaining the GeneChip fluidics station.

Microarray Suite 5.0 Manual  The Affymetrix® Microarray Suite software is part of the Affymetrix® GeneChip® instrument and probe array platform. This manual explains how to use Microarray Suite to control the GeneChip® Fluidics Station 400,the Agilent GeneArray® Scanner, and analyze experimental data for GeneChip probe array assays, including generating reports that summarize intensity data, analysis output, and algorithm settings.

MicroDB 3.0 Manual  This manual discusses how to use this software package that converts Affymetrix GeneChip data to a format that makes it publishable to a database and the database model that Affymetrix uses

BimCore's Affymetrix Quick Guide  A quick summary of instructions for the novice user of Affymetrix’s Microarray Suite 5.0 Software. This quick guide based on Affymetrix’s anaylsis manual, goes through the steps necessary to ascertain data quality and the obtain initial lists of probes that have increased or decreased in expression signal.

GeneChip Expression Analysis Manual  This manual is a continuation of the Expression Analysis Technical manual and goes into more detail about experimental design, statistical analysis, and biological interpretation of microarray data. (released 2003)

GeneChip Operating Software Manual