Here is a "best of" collection of links to manuals and tools for Microarray workflow. For other instruments refer to Collection of Support Documents
Collection of Microarray Resources
For SureScan Dx Microarray Scanner resources, please see here
SureScan Microarray Scanner
General
G4900DA SureScan Microarray Scanner System User Guide
Agilent Microarray Scanner Software Versions A.8.3 Release Notes
Agilent G2565BA Microarray Scanner Bar Code and Glass Specifications
Technical and Application Notes
A Method for Quantifying the Performance of a DNA Microarray Scanner
CGH + (SNP) Microarray Analysis Platform
General
Oligonucleotide Array-Based CGH for Single Cell Analysis - Enzymatic Labeling Protocol - User Manual
Oligonucleotide aCGH for Genomic DNA Analysis - ULS Labeling - User Manual
Technical and Application Notes
Microarray Gene Expression Platform
General
eArray site for Downloads
Gene Expression Microarrays
One-Color Microarray-Based Gene Expression Analysis - User Manual
Two-Color Microarray-Based Gene Expression Analysis - User Manual
Exon Microarrays
One-Color Microarray-Based Exon Analysis - LIQA WT Labeling Protocol 2.0
Two-Color Microarray- Based Exon Analysis - LIQA WT Labeling Protocol 2.0
Technical and Application Notes
Gene Expression
Exon Microarrays
Comprehensive coverage with the Agilent SurePrint G3 Exon Microarray system
Whole Transcript Profiling Using SurePrint G3 Exon Microarrays in a Complete Workflow
Highlights from The WINTHER trial (NCT01856296)
Microarray miRNA Platform
General
miRNA Microarray System with miRNA Complete Labeling and Hyb Kit - User Manual
Technical and Application Notes
Exosome miRNA Profiling with the Agilent miRNA Microarray Platform
MicroRNA Analysis of Archival FFPE Samples by Microarray
Agilent Human, Mouse, Rat, and Custom miRNA Microarrays