AMC Converts to GCOS (11/10/04) - The AMC is now using GeneChip Operating Software (GCOS) to process, analyze and package data. This document summarizes what has been done and how it affects OHSU investigators.

Sample Pooling for Microarray Analysis: A Statistical Assessment of Risks and Biases (11/10/04) - A Technical Note from Affymetrix's website that discusses sample pooling, an experimental condition many investigators encounter.

AMC Hybridization Naming Schema (1/30/04) - Need help understanding hybridization names? This links to information about how the AMC names hybridizations and why the schema is used.

Agilent Bioanalysis Interpretation (11/05/03) - The AMC uses the Agilent bioanalyzer to check RNA quality. This file explains the results of the bioanalysis

Affymetrix MAS 5.0 Statistical Algorithm - Appendix from Affymetrix Manual describing the satistical algorithm that is used to generate signal metrics from raw images

Affymetrix: Data Analysis Fundamentals from Affymetrix Explains the basics of Genechip analysis as well as providing useful information about probeset names

AMC Labeling Methods v1.0, Standard Labeling Assay This document provides a brief description of methods used in the AMC laboratory for sample labeling and array hybridization and processing during the period of Jan 2002 through June 2004. It describes the AMC standard labeling assay and hybridization methods for GeneChip arrays with feature sizes greater than or equal to 18 micron (e.g, HG-U133A, MOE430A, MG-U74A). If you have any questions about the methods or require additional information, please contact Kristina Vartanian or Chris Harrington. Please note: for sample inputs of less than 4 ug or assays with GeneChip 2.0 all-on-one arrays, the protocols described in this document are not accurate. For publication, we recommend confirming final methods text with a member of the AMC staff.

AMC 3'IVT Expression Assay Methods 2.0, Affymetrix Kit Labeling Assay. This document provides a brief description of methods used in the AMC laboratory for sample labeling and array hybridization and processing during the period of June 2004 through September 2007. It describes the AMC standard labeling assay and hybridization methods for GeneChip arrays with feature sizes greater than or equal to 11 micron (e.g, HG-U133 Plus 2.0,MOE 430 2.0). If you have any questions about the methods or require additional information, please contact Kristina Vartanian or Chris Harrington.

AMC Methods 3.0, Small Sample, Affymetrix Kit Labeling Assay. Contact Chris Harrington.

More Coming Soon