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Mathematical and Statistical Computing Lab

Developed by: Jennifer J. Barb and Peter J. Munson

  • The MSCL Analyst's Toolbox is a set of scripts that provide a wide variety of data transformation, normalization, statistical testing and gene selection capabilities which complement the extensive capabilities of the JMP statistical discovery software package. Combined with JMP, these scripts provide a powerful, flexible, interactive and highly economical way to analyze results from small or large microarray studies. Although the scripts are primarily formatted to analyze Affymetrix data, they can be used with a wide variety of microarray platforms. The scripts are designed to give users high flexibility in the analysis of their data and can be customized as needed. The scripts can be used on the PC, Linux or MacIntosh. (Menu bar item functionality is enabled only on the PC. Please read README instructions in the download folder for details.)

    NIH staff please go here

    MSCL Toolbox Scripts - includes all Toolbox scripts
    MSCL Toolbox User's Guide User's Guide - includes a brief "how-to" description of running MSCL toolbox scripts.
    Course Notes Day 1 notes - includes description of the Toolbox
    Day 2 notes - includes statistical background information and more in depth info on the Toolbox
    Two-Way ANOVA notes - includes background info on Two-Way ANOVA script
    Alternative Splicing notes - includes background info on alternative splicing and ExonANOVAnested script
    GO-SCAN notes - includes information on Gene Ontology and the GO-SCAN bioinformatics tool.
    Affy Expression Console notes - includes directions on exporting .CEL files from EC as text files
    Example Tables Test tables - includes examples for use with learning how to use the MSCL toolbox
    Affymetrix Annotations Annotation files - Affymetrix annotation in JMP table form.

  • CIT course Statistical Analysis of Microarray Analysis using The MSCL Analyst's Toolbox and JMP.
    This course, offered twice per year over the past few years teaches students how to use the MSCL Analyst's Toolbox. The course includes an introduction to the toolbox, an introduction to JMP and a hands-on demo. Newly added to the course is an introduction to visualization tools in JMP. Please check the course description found on the CIT website for a detailed description of the course.

    Last updated: June 4, 2009
    Peter Munson: mail
    Jennifer Barb: mail

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