We at Affymetrix understand that getting the most out of your experiments using
GeneChip® Arrays depends on the available software tools to manage and analyze your microarray data. As the applications for Affymetrix GeneChip®
Arrays continue to grow in number, the available software tools also evolve in both variety and scope. Although it is always comforting to have the ability to choose
the right tools for the job, such a variety of informatics solutions represents yet another decision to research. To help you select the right software tool for your
needs, Affymetrix has collected below a series of applications.
Explore the Software Solutions Catalog
Applications which display the “AGCC Ready” logo can handle the new file formats used by both Affymetrix GeneChip Command Console (AGCC) and Expression Console.
APPLICATION CATEGORY - EXON EXPRESSION
Exon analysis involves generating signal estimates from input CEL files at either the gene or exon level. Gene level estimates can be leveraged using traditional expression workflows. Exon signal estimates can be combined using a variety of gene models used to predict potential transcript forms. Comparing how these forms might differ within a collection of samples leads to predictions of alternatively spliced transcripts. The dynamic nature of genome builds and annotation information used in gene models can increase the complexity of exon expression analysis. Applications within this category have been specifically built to handle these types of investigative questions.
XRAY is the only available Excel add-in for expression that can rapidly normalize and analyze large numbers of (binary XDA format) CEL files. XRAY is also unique in that it simultaneously implements gene-level and exon (alternative splicing) studies, while also simultaneously using all six million probes at every stage of analysis. All controls and results are in Microsoft Excel so users are automatically familiar with controls and worksheet project organization.
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Mixed Model ANOVA Detects Differential Alternative Splicing and Gene Expression even when data has dependencies.
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XRAY's project construction wizard and use of the familiar Excel interface allows users to work immediately with little software product training.
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XRAY runs on regular desktop and laptop computers (at least 700 MHZ with 500 MB RAM).
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Fixed memory implementation means that practically unlimited numbers of CEL files can be analyzed simultaneously.
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XRAY is powerful enough to handle all the data on a chip with no filtering (but DABG and probe set annotation level filters are available).
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XRAY Data visualization is the only system that simultaneously shows genomic, transcript cluster, probe-set, probe annotation and expression in a single view.
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Automatic annotation and links to public and NetAffx databases.
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Validated statistical analysis.
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XRAY is efficient. Quantile normalization and expression analysis for 20 CEL files runs in around 10 minutes on standard desktop computers (the application never requires more than 250MB ram).
To get more information or to contact sales directly, please contact 775-787-9902 or email xray@biotiquesystems.com.
View a pre-recorded product demo on XRay v2.2, created in March 2007 (10 minute)
Genedata Expressionist® is a modular enterprise system for biomarker discovery. It represents a single-point-of-access for experimental, proprietary and public data, including sample information, raw and pre-processed transcriptomics, proteomics, metabolomics and lab chemistry data, analysis results, reports and documentation.
Expressionist's dedicated Refiner Array module performs automated quality assessment and pre-processing of Affymetrix GeneChip® Exon data. Automated data pre-processing saves time, resources and cost in microarray analysis. Standardized workflows increase reproducibility and enable efficient, high-throughput processing of large experimental datasets. Performance benchmarks demonstrate nearly linear scalability when processing 50, 100, 500 or 1'000 Exon chips with Genedata Expressionist, and nearly optimal parallelization of CPUs (tested up to 32 CPUs, e.g. exon chip processing – background subtraction, quantile normalization and RMA – takes 3.3 seconds with a 4 CPUs configuration!) Comprehensive reporting and documentation features ensure effective project management and communication. Read more about Refiner Array.
The Genedata Expressionist® Analyst module features powerful algorithms and intuitive visualizers for efficient analysis of transcriptomics, proteomics, metabolomics and lab chemistry data. A flexible workflow system allows for standardized data analysis and convenient communication between bioinformaticians, computational biologists, statisticians and bench scientists. Finally, an open framework built on scalable enterprise architecture sets the basis for integration into any IT environment and extension with in-house algorithms, tools and databases. Read more about Analyst.
Microarray analysis and annotation software working with Affymetrix raw data files. ChipInspector carries out significance analysis on the single exon probe level. Exon probes with significant expression ratios are annotated based on the Genomatix proprietary genome annotation and analysis system ElDorado. Based on the annotation result, probes are assigned to transcripts. Graphical representations of the gene loci, include the display of alternative transcripts as well as probe to exon mapping. Particularly when analyzing Exon Arrays, this allows identification of differentially regulated transcripts and potential new splice variants. Several clustering features allow to group exon probes with similar profiles. Results can easily be exported to Genomatix BiblioSphere PE for analysis of relations between expressed genes.
JMP® Microarray, a desktop statistics tool for Affymetrix Exon Array analysis is an integrated environment for accessing discovering, analyzing, and exploring data patterns that can lead to the key molecular insights, for example, identification of biomarkers for promising new drugs. It uses JMP software as a powerful and dynamic data visualization and statistical analysis desktop client to SAS. Nearly 100 genomics processes employ JMP's Scripting Language (JSL) to launch open and customizable SAS macro programs in the background, enabling unparalleled data processing and statistical capabilities for rigorously understanding patterns and discoveries.
JMP Genomics offers intuitive and proven Design of Experiments (DOE) tools for creating efficient and unconfounded experiments. After running the experiment, Affymetrix Exon array data can be uploaded from .CEL files, or .txt files from Expression Console analysis can be directly imported using JMP Genomics' utilities. Quality control and normalization can be performed with a variety of routines, and then statistical modeling and significance testing can be performed using an efficient ANOVA for simple experimental designs, or a mixed-model ANOVAs for more complex experimental designs and models. The latter are especially useful for detecting alternative splicing. In summary, JMP Genomics offers. a wide range of input processes for popular genomic instrumentation; deep and broad statistical methods that optimize tradeoffs between sensitivity, specificity, and reproducibility; and integrated links to many current bioinformatics annotation tools and websites including NetAffx, KEGG and Ingenuity.
View a pre-recorded product demonstration. (7 minute)
Partek Genomics Suite is an integrated statistical and visual analysis solution for GeneChip® experiments, optimized for fast and memory-efficient processing of large, ultra high-dimensional data. Proven, rigorously tested statistical methods are integrated with 2-D and 3-D interactive visualization allowing you to reliably explore, identify, and present important patterns in your data. The Partek Genome Browser™ provides dot plots, box & whiskers, profiles, exon-level, gene-level, and alternative splicing summaries. All graphs can be exported in publication-quality vector graphic format. Multiple classification methods are integrated with gene selection for accurate diagnostic/prognostic prediction. Seamless integration with .CEL, .CDF, .CHP, and .EXP files includes fast, memory-efficient RMA and probe-level import. Partek GS automatically annotates all results and provides hyperlinks to NetAffx and other internet databases.
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