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Nov 10, 2016

JMP Genomics User Guide Has Been Updated

Our goal at JMP Genomics has always been to make it easier for you, the genomics scientist, to analyze and interpret your data. The JMP Genomics User Guide has been there to help you choose which analytical process(es) best meet your needs by showing you what you need to run each process and, through the use of an illustrative example, how to evaluate and interpret your results. This documentation has grown and evolved as JMP Genomics has grown and evolved. We’re proud to announce and make available to our users the newest edition of the JMP Genomics User Guide.


This update to the JMP Genomics User Guide combines and extends the best features of the original JMP Genomics User Guide and the JMP Genomics User Guide – Supplement that you received with JMP Genomics. Existing chapters have been revised, and new chapters have been added. All chapters have been fully updated with detailed illustrations and explanations for our current version, JMP Genomics 3.2.


The updated JMP Genomics User Guide is divided among the nine different volumes listed below:


  • Getting Started with JMP Genomics. This manual lists installation instructions and requirements, provides a brief introduction to JMP Genomics and this documentation, and detailed descriptions and instructions for setting up and using the basic JMP Genomics workflows. This manual also provides a troubleshooting guide, various appendices, a comprehensive glossary and a complete reference list for all of the manuals.

  • Designing Experiments with JMP Genomics. This manual describes how to use JMP’s DOE functions to design your experiment and generate an experimental design file, which is the first step in your analysis.

  • Data Import and Manipulation with JMP Genomics. This manual provides detailed descriptions of the different types of data sets used by JMP Genomics, how to import data from different sources, and how the resulting data sets can be manipulated and transformed into formats appropriate for specific analyses.

  • Genetic and Copy Number Analysis. This manual provides detailed descriptions for manipulating genetic data sets, determining specific marker statistics, carrying out various association tests, assessing linkage, mapping quantitative trait loci, and performing haplotype and copy number analyses.

  • Microarray Analysis. This manual lists and describes a multitude of procedures for performing quality control on your data, normalizing it, looking for patterns, fitting statistical models to the observations and comparing the aggregated results.

  • Predictive Modeling. Can your data be used as the basis for making predictions of future experiments? This manual details a number of different predictive models as well as procedures for comparing the relative efficacy of the different models with your data.

  • Annotation Analysis. Once you have identified one or more significant genes, you must determine the biological significance of those genes. This manual provides tells you how to use JMP Genomics tools to incorporate biological meaning with your statistical results.

  • Spectral Preprocessing and Analysis. This manual describes the JMP Genomics processes that are useful for analyzing two dimensional and three-dimensional spectra.

  • Programming Guide. This manual provides an introduction to building and programming your own analytical processes. Processes you create can be added to the JMP Genomics menu.

  • To access this updated resource, just download the zipped file from the JMP Genomics Web site, unzip it and copy it into your JMP Genomics documentation folder. After you install it, you can access all nine volumes as before: Just select Genomics > Documentation and Help > User Guide to go to the User Guide entry page. From this portal, just click on the appropriate link to go to a specific manual. Each manual is dynamically cross-referenced to each of the other manuals – just follow the links embedded in the chapters to access the additional information you need.


    Registered users of JMP Genomics should watch their Inboxes for an e-mail containing instructions on how to download and install the latest update to the JMP Genomics User Guide.

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