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    TIBCO Spotfire DecisionSite for Microarray
    Analysis

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  DecisionSite for Microarray Analysis (DSMA) is an advanced
    application for the analysis of microarray experiments. Product
    provides a comprehensive set of data access, processing,
    normalization and analysis methods for data derived from both
    Affymetrix and two-channel technologies. By embedding analysis
    starting points and customizable tools into redistributable workflows
    called 'Guides', new users can become productive quickly. Built-in
    quality control (QC) capabilities provide fast filtering of the data that can
    be used to limit the results set used in further analysis and remove
    potential bias. Analysis can be customized into a series of Guides
    allowing the user to choose from a number of advanced analysis
    paths, including methods for pattern detection, differential expression
    testing, gene list comparison and incorporation of annotations.

    DSMA is powered by S-PLUS to provide multiple methods of probe
    level analysis, normalization, quality assessment and advanced
    statistics for secondary analysis of both Affymetrix and 2-Channel
    microarray experiments.

    DSMA features/capabilities include:

    1) Direct access to Affymetrix cell intensity (CEL) files and summarized
    expression values (CHP files), databases and alternative methods for
    processing and normalization of probe level data.

    2) Access to spotted array data, within and between chip normalization
    for two-channel data.

    3) QC summary reports to assess RNA degradation, within condition
    reproducibility and between array distribution alignment.

    4) Quality control steps provide the ability to flag bad experiments and
    remove them from further processing to eliminate bias.

    5) Interactive annotations and Gene Ontologies (GO) are added to the
    analysis to provide functional insight into interesting markers.

    6) Multifactor analysis of variance (ANOVA) with treatment contrasts to
    identify statistically significant, differentially expressed markers based
    on experimental design.

    7) Filtering of differentially expressed markers based on fold change,
    differential expression significance and expression intensity patterns
    across arrays and experimental conditions.

    8) Comprehensive error rate corrections to control false positives in
    differential expression testing.

    9) Support for minimum information about a microarray experiment
    (MIAME) standards by annotating analysis datasets with experimental
    details.

    10) Cluster analysis methods, including hierarchical, K-means, self-
    organizing maps (SOMs), partitioning around medoids (PAM) and
    model-based.

    11) Principle Component Analysis (PCA) on markers and/or arrays.

    12) Management and comparisons of lists with Venn diagrams and
    Boolean operations.

    The application can be extended to interactively incorporate custom
    statistical methods written in other packages. The DecisionSite
    Analytics Server, which includes the Computation Services framework,
    can utilize existing expertise implemented in environments such as
    SAS (see G6G Product Number 20007), Insightful (see G6G Product
    Number 20062) and (see G6G Product Number 20064), SciTegic (see
    G6G Product Number 20063), or R open source with Bioconductor
    methods and libraries. By providing an extendable platform capable of
    communicating with external statistics providers, DSMA coupled with
    Computation Services becomes a comprehensive microarray analysis
    solution for today and for the future.

    System Requirements  

    Operating System
    Microsoft Windows 2000 Professional SP4
    Microsoft Windows XP Professional and Home Edition SP2
    Microsoft Windows XP 64-bit Edition SP2

    NOTE: Spotfire DecisionSite for Microarray Analysis 9.1.0 is not
    supported on Microsoft Windows Vista

    Spotfire Software
    Connection to Spotfire Analytics Server 8.1 or higher via Spotfire
    DecisionSite Client 8.1.1 or higher.  

    Client-side RAM
    256 MB (recommend 512 MB or greater)

    User Permissions
    Spotfire DecisionSite for Microarray Analysis must be installed and run
    under a Windows user account with "Administrator" permissions.  

    Manufacturer   Home office; see web site for international locations.

    TIBCO Spotfire, Inc.
    212 Elm Street
    Somerville, MA 02144
    U.S.A.Telephone +1.617.702.1600
    Fax +1.617.702.1700
    Toll-Free +1.800.245.4211
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