Affymetrix Arrays

GeneChip Operating System (GCOS)

GCOS (Affymetrix) software automatically acquires and analyzes image data and computes an intensity value for each probe cell from the resulting *.dat/*.cel file via MAS5 algorithm. For gene expression applications, GCOS provides single or batch analysis of expression arrays, allows one to visualize the resulting scans and is required for use of other Affymetrix analysis software applications (e.g. GTYPE). Users may download the GCOS software free directly from Affymetrix.

Expression Console

Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression and Exon Arrays. The Expression Console workflow provides the user with a choice of the more commonly used Probe Set summarization algorithms, such as MAS5, PLIER and RMA. Additionally, GeneChip data quality control (QC) can readily assessed using the various QC generated tables, visualization and graphing tools provided by the Expression Console software. The Expression Console software may be downloaded for free directly from Affymetrix.

Data Transfer Tool (DTT)

Affymetrix’s GeneChip Data Transfer Tool (DTT) is a wizard-driven software application. It will lead you through the process of creating DTT Archive, Flat, or CAB files and enables the sharing of GeneChip data across GeneChip systems with different versions of GeneChip Software. DTT must be used when transferring GCOS v1.2 (or higher) — generated data to other GCOS users or to users of MAS 5.0 and higher, featuring control of all aspects in importing, exporting, backup of and restoring GCOS generated data files.

ArrayAssist Lite

The ArrayAssist Lite (Affymetrix) software package enables one to easily generate Affymetrix GeneChip® expression data measurements and reports. This software application is supported by Affymetrix (offered free in conjunction with Stratagene). It features four of the latest generation of probe-level analysis methods. ArrayAssist Lite includes Probe Logarithmic Intensity Error (PLIER) estimation, resulting in better sensitivity and precision for accurate gene expression values from low-intensity signals. It also supports other gene expression algorithms such as Robust Multi-chip Average (RMA) analysis, GC-RMA, and the Affymetrix Microarray Suite v.5 (MAS5).

Cyber-T 

Following any necessary adjustments of your collected data results (baseline/background corrections, normalizations, etc.), Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic. Cyber-T is a web-based program, written at UC Irvine, that employs statistical analyses based on simple t-tests that use the observed variance of replicate gene measurements across replicate experiments, or regularized t-tests that use a Bayesian estimate of the variance among gene measurements within an experiment.

GeneSpring GX

GeneSpring GX (Agilent Technologies) is a commercial software application that displays expression data in ways that help you conceptualize the information in your data. This feature rich software product is available for users at the Facility on a fee for usage basis. First time users of this software are encouraged to download a free trial version of the software from Agilent Technologies to their own computer once they have all of their data ready for analysis. This way they can practice and begin to learn the basics of this software application prior to starting with the Facility’s copy, which is accessed on a fee for usage basis.

PathwayArchitect

PathwayArchitect (Stratagene) is a commercial software package, which allows users to build Biological Interaction Networks (BINs) based upon your list of genes/proteins of interest from your microarray experimental data. This software allows users to addresses the question, "what molecules are connected to the biological objects in my list?" in order to tease out the relevant pathway or interaction relationships found within your data. Use of the Facility’s copy of this software application is accessed on a fee for usage basis.

Exon Array Computational Tool (ExACT)

The Affymetrix Exon Array Computational Tool (ExACT) software package enables probe level analysis of Affymetrix exon arrays. It allows users to 1) normalize exon array data, 2) compute exon level signal estimates, 3) compute gene level signal estimates, 4) merge the results with annotations from NetAffx and 4) derive expression graph files for visualization of exon array results within IGB (Affymetrix’s Integrated Genome Browser).

Integrated Genome Browser (IGB)

The Integrated Genome Browser (IGB, pronounced ig-bee) is a free application/tool intended for visualization and exploration of genomes and corresponding annotations from multiple data sources Download a copy of the software directly from Affymetrix. Please read the additional requirements section found on the download page. The IGB User Guide provides detailed information on how to properly make the most of this application.

GeneChip Genotyping Analysis Software (GTYPE)

Affymetrix GeneChip Genotyping Analysis Software (GTYPE) is part of the GeneChip Mapping Array System, specifically designed to give accurate, automated SNP allele calls for the GeneChip Mapping Arrays, the 10K array, 100K array set and 500K array set. GTYPE is an evolution of the earlier GeneChip DNA Analysis Software (GDAS). The manual for GTYPE describes the particular attributes and proper use of this software analysis application.

BRLMM Analysis Tool (BAT)

The Affymetrix BRLMM Analysis Tool software package allows for the installation of BRLMM (pronounced "B-realm"), an improved genotype calling algorithm for Affymetrix genotyping arrays such as the GeneChip® Human Mapping 100K & 500K Array Sets. BRLMM is an evolution of the RLMM genotype calling algorithm of Rabbee and Speed, [2006]. BRLMM performs a multiple-chip analysis fitting probe effects to increase precision on signal estimates for the two alleles of each SNP, followed by a Bayesian classification approach to make genotype calls. The details of the model and typical performance are described in full in a white paper.

The BRLMM Analysis Tool provides a simple-to-use Graphical User Interface (GUI) to run the BRLMM method on Microsoft Windows. The details of the updated 500K data analysis workflow using BRLMM, including step-by-step instructions to install and run the BRLMM Analysis Tool are described in a workflow document. Further details can be found in a manual, which serves as a manual for both the BRLMM Analysis Tool and for the command line implementation, apt-probeset-genotype.   

Copy Number Analysis Tool (CNAT)

The Affymetrix Chromosome Copy Number Analysis Tool (CNAT) enables the identification of genome-wide chromosomal gains and losses using the GeneChip Mapping Arrays and Whole Genome Sampling Assay. Download a copy of the software directly from Affymetrix.   

Affymetrix NetAffx

The NetAffx Analysis Center is an integrated, online informatics resource, created by Affymetrix to assist genomic researchers with the design and analysis of RNA/DNA array-based experiments. Those interested in optimally utilizing this highly informative, web-based resource can download a copy of the NetAffx User Manual to learn the proper ways to search and retrieve extensive annotations; array content and/or specific probe sequences.

Tiling Analysis Software (TAS)

Tiling Analysis Software (TAS) is a freely downloadable tool provided by Affymetrix for analysis, with which one can 1) perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, 2) can derive an interval overlap report and/or computation of summary statistics, which can be readily imported into Affymetrix’s Integrated Genome Browser (IGB) tool for visualization against genomic annotations. The TAS User Guide provides detailed information on how to properly utilize this application.