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    ArrayAssist Advanced Software

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  ArrayAssist Advanced Software, powered by avadis, is a
    comprehensive software solution for the analysis of microarray gene
    expression data. It offers a full spectrum of advanced analytical features
    and dynamic interactive visualizations to help you analyze results from
    both 3’ in vitro transcription (IVT) expression microarrays and new
    microarray platforms. Data can be imported from leading array platform
    technologies (Applied Biosystems, Affymetrix, Agilent, CodeLink,
    CombiMatrix and Illumina) and from several scanner formats (GenePix,
    ImaGene, ScanAlyze and QuantArray) or you can build your own custom
    templates. It offers  customized workflows for Affymetrix and Illumina
    arrays. Single-dye and two-dye experiment workflows are also
    provided. These workflows allow you to step-by-step define
    experimental groupings, perform primary analysis and quality control,
    perform significance analysis, cluster the data, explore the biological
    annotation for each significant gene and map those genes onto the
    genome in the integrated genome browser. In addition to the guided
    workflows, a full spectrum of advanced analytical features such as
    statistical tests (multi-way ANOVA and non-parametric statistical tests),
    data mining tools (classifiers for machine learning-based prediction)
    and advanced, dynamic, interactive visualization options are also
    available.

    ArrayAssist Advanced Software additional features are:

    Clustering and Visualization Tools - 1) Multiple clustering options
    including k-Means, hierarchical, EigenValue, self organizing maps
    (SOM), random walk and principal components analysis (PCA); 2)
    Multiple, interactive views of clustering results including clusterSet view,
    Dendrogram view, and the similarity image view; 3) Multiple
    visualization tools including spreadsheet, scatter plot, 3D scatter plot,
    profile plot, heat map, histogram, profile match, spot image, annotation
    view, matrix, summary statistics, and bar chart; 4) Interactive Genome
    Browser; 5) One-click export of plots and tables to Excel for further
    analyses.

    Statistical Analysis Tools - 1) Multiple one-click statistical tests: t-tests,
    Mann Whitney tests, multi-way ANOVA, and repeated measures test; 2)
    Multiple p-value generation via permutations or asymptotic analysis,
    comprehensive testing corrections including false discovery rate (FDR)
    and family-wise error rate (FWER) control; 3) Volcano plots for
    interactive filtering based on significance and fold change; 4) Integrated
    into the R statistical package offering a host of statistical functions.
    Classification and Prediction-Based Modeling - 1) Classification tools
    to exploit experimental data for learning-based prediction of outcomes
    including decision tree (DT), neural network (NN), support vector
    machine (SVM), naïve Bayesian (NB); 2) Linear multivariate regression
    algorithm allows for prediction of continuous variables like survival
    indices.

    Splicing Analysis of Affymetrix GeneChip Exon Arrays - ArrayAssist
    Advanced software includes a focused workflow for Affymetrix
    GeneChip Exon Arrays that guides you through the process of
    identifying which genes are transcription regulated and which are
    splice regulated and which are regulated by both. Specific features
    include - 1) One-click PLIER and Robust Multichip Analysis (RMA)
    algorithms to generate gene level and exon level values; 2) Splicing
    index is determined (exon signal/gene signal); 3) Comprehensive
    quality reporting including native Affymetrix RPT file generation and
    experimental quality metrics based on Affymetrix internal controls; 4)
    Identifiers include probe-set ID, Exon ID and transcirpt cluster ID 5)
    Integration of Gene, Exon and Splice index in ArrayAssist Exon Master
    Data Table for follow-up analysis; 6) Quality metrics include - intensity
    distributions, relative intensity distribution, MAD residuals and DABG
    values; 7) Visualization tools include: boxplots, PCA, Histograms,
    Trellis plots.

    Copy Number & Loss of Heterozygosity Analysis - 1) Guided workflow
    for comprehensive Copy Number analysis, Quickly identify
    amplifications, deletions, and Loss of Heterozygosity (LOH) regions, 2)
    Integrates expression, splicing, promoter binding and copy number
    data in a single intuitive software package.

    Note: Detection of DNA regions with an abnormal gain or loss enables
    the identification of critical genes and pathways responsible for the
    development and progression of a particular disease. Copy number
    analyses are usually performed using whole genome mapping arrays
    to determine regions of chromosomal deletion, amplification, or LOH.
    Since the experiment involves mapping the whole genome the result
    data can be both large and complex. To help you more easily identify
    important regions for further study, ArrayAssist Advanced provides you
    with a guided workflow for comprehensive analysis of data from
    Affymetrix Genechip Mapping Arrays. The step-by-step process helps
    you quickly identify amplifications, deletions, and LOH regions from
    your expression data. Results can be displayed in a variety of views that
    are linked so that selection in one view is reflected in another.

    Gene Annotations - 1) Automatic download of current gene annotations
    for all Affymetrix GeneChip microarrays based on the latest NetAffx
    annotation; 2) Workflows to automatically retrieve and view gene
    information from web sources including Unigene, EntrezGene, NCBI,
    SOURCE, BLAST, PubMed, and SGD; 3) Annotation engine offers other
    functionalities such as PubMed correlation matrix, Gene Ontology (GO)
    browser and GO cluster and more.

    System Requirements  

    Operating System: Fedora Core release 5 Linux, Macintosh OSX
    (universal binary support), Microsoft Windows XP, or Windows 2000.
    Processor: Intel® Pentium® 4 with 2.0 GHz
    Memory:2 GB RAM
    Disk space: 120Mb for install. We recommend several additional GB for
    the analysis itself. Exact disk space depends on project size.

    Manufacturer   Home office; see web site for international locations.

    Stratagene (part of Agilent Technologies, Inc.)
    11011 N. Torrey Pines Road
    La Jolla, CA 92037
    (858) 373-6300

    Customer Service:
    Toll Free: (800) 424-5444
    Cedar Creek, Texas: (512) 321-3321
    Fax Orders: (512) 321-3128

    Technical Services:
    Toll Free: (800) 894-1304
    Fax: (858) 535-0034
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