New in JMP® Genomics 3.2

JMP Genomics delivers to the desktop the graphical and analytic capabilities required by scientists working with large genomics data sets. JMP Genomics provides biologists and biostatisticians with flexible, menu-driven platforms to access, evaluate, analyze and explore data interactively to discover biologically relevant patterns. This all-in-one genomics software is built upon the SAS®9 and JMP 7 platforms.

JMP Genomics 3.2 includes new Basic Workflows that streamline analysis of genetics, copy number and expression data. This release also includes new support for copy number CHP files from Affymetrix Genotyping Console and significantly enhanced features for importing expression data from Illumina BeadStudio software. JMP Genomics 3.2 introduces the option to perform GCRMA background correction on CEL files. Significant enhancements to genetics processes also greatly reduce the time required to filter and analyze genotype data. JMP Genomics 3.2 Release Notes (PDF) include details about these and other new features.

The JMP Genomics 3.2 update is now available for customers currently using JMP Genomics 3.0 or JMP Genomics 3.1. If you are a licensed JMP Genomics customer and have not yet requested JMP Genomics 3.0, please request your complimentary upgrade.

JMP Genomics 3.2 adds new capabilities to the JMP Genomics platform and enhances previously introduced features:

• New! Affymetrix Experimental Design Wizard
• New! Basic Workflows for Expression, Genetics, Copy Number and Exon Analysis
• New! Affymetrix CN CHP Input Engine
• New! Missing Genotype by Trait Summary
• New! Support for QTL Analysis
• New! Survival Analysis
• New! Learning Curves
• New! Kinship Matrix
• New! GEO Submission Tool
• New! Partial Correlation Diagram
• New! Data Stack
• Enhanced! Affymetrix CEL Input Engine adds GCRMA
• Enhanced! Genetics Processes
• Enhanced! Action Buttons for One-Way ANOVA, ANOVA and Mixed-Model Analysis
• Enhanced! Illumina Expression Input Engine
• Enhanced! Performance of Genetics Processes
• Enhanced! Genetic Marker Properties

New! Affymetrix Experimental Design Wizard

Assists in creating a design file for a set of SNP or expression CEL or CHP files. This interactive wizard can create a design file from paired ARR and data files or an existing text or Excel file that lists names of the data files. After the design file is created, it is automatically loaded into the appropriate import process.

New! Basic Workflows for Expression, Genetics, Copy Number and Exon Analysis

Incorporates options from multiple processes in a simplified dialog and automatically builds a workflow behind the scenes using the JMP Genomics Workflow Builder. Workflows incorporate various processes, including quality control, filtering, normalization and modeling. Basic Exon Workflow automatically creates a model to test for alternative splicing.

New! Affymetrix CN CHP Input Engine

Imports and combines Affymetrix CN CHP files created by Affymetrix Genotyping Console Version 2 into a single SAS data set. The imported data set may be launched directly into the Basic Copy Number Workflow.

New! Missing Genotype by Trait Summary

Tests whether missing genotypes at a particular genetic marker are related to a trait. Use interactive plots of results to view differences in missing value patterns between cases and controls.

New! Support for QTL Analysis

An experimental QTL Mapping submenu has been added to the main Genomics menu. In addition, a new WinQTLCart Input Engine lets users import a Windows QTL Cartographer .MCD file into a SAS data set containing marker genotypes and traits, and a SAS data set containing annotation information. Processes for single marker analysis, combined interval mapping, and a utility for building QTL genotype probability data sets also are new.

New! Survival Analysis

Tests association of each row of the input data set with a censored response, fitting a Cox proportional hazards model on a row-by-row basis to a normalized data set.

New! Learning Curves

Employs cross-validation to evaluate a model using different sample sizes, thereby revealing the influence of sample size on accuracy and variability of the model. A wide variety of distance metrics are available for making the predictions.

New! Kinship Matrix

Creates a matrix containing either kinship coefficients or covariance coefficients between pairs of related individuals. These coefficients can then be used as random effects in order to analyze family data in an association setting, using processes (e.g., Marker-Trait Association, SNP-Trait Association) that can accommodate random effects.

New! GEO Submission Tool

Formats an experiment for submission to the Gene Expression Omnibus (GEO) database. Data is placed in MiniML format and written to an .XML file for batch submission to GEO.

New! Partial Correlation Diagram

Infers potential relationships between variables by plotting each one as a node and connecting the nodes with line segments.

New! Data Stack

Converts tall SAS data sets and information from an experimental design file into a singled stacked data set. This new feature includes an option for subsetting the data, using the first n rows, for preliminary testing. This is particularly useful for SAS programmers who wish to convert a tall data set from JMP Genomics into a stacked format for SAS PROC MIXED.

Enhanced! Affymetrix CEL Input Engine adds GCRMA

JMP Genomics 3.2 introduces the option to perform GCRMA background correction on large sets of Expression CEL files. Performance of RMA normalization during CEL import has also been significantly improved.

Enhanced! Genetics Processes

Allows users to specify that all markers are biallelic and trigger a faster implementation of case-control association. A time-saving PCA Data Set option allows users to rerun PCA population stratification analyses without having to repeat the principal component calculations.

Enhanced! Action Buttons for One-Way ANOVA, ANOVA and Mixed-Model Analysis

New Action buttons launched with the output of JMP Genomics ANOVA processes add the ability to subset the data in either wide or tall formats. Additional options allow users to construct one-way plots for selected rows and fit models to the input data for selected rows for more complex models.

Enhanced! Illumina Expression Input Engine

Adds the ability to select columns to import, an option to apply Log2 transformation to intensities, options to filter intensities based on detection p-values, and options for annotation data output.

Enhanced! Performance of Genetics Processes

Major performance enhancements reduce computation time and use less memory in numerous genetics processes, including Marker-Trait association, SNP-Trait association, Recode Genotypes and TDT.

Enhanced! Genetic Marker Statistics

Enhanced marker properties output includes interactive distributions of minor allele frequency (MAF plots) and missing genotype proportion plots. These plots may be generated for the entire data set or annotation group.

Affymetrix and GeneChip are registered trademarks owned or used by Affymetrix, Inc. GeneChip-compatible is a trademark owned or used by Affymetrix, Inc.

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