Release Notes. JMP Genomics. Version 2.0.3

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1 JMP Genomics Version Release Notes Creativity involves breaking out of established patterns in order to look at things in a different way. Edward de Bono JMP. A Business Unit of SAS SAS Campus Drive Cary, NC

2 Release Notes for JMP Genomics Release Notes for JMP Genomics Copyright 2006, SAS Institute Inc., Cary, NC, USA All rights reserved. Produced in the United States of America. Your use of this publication shall be governed by the terms established by the vendor at the time you acquire this publication. U.S. Government Restricted Rights Notice: Use, duplication, or disclosure of this software and related documentation by the U.S. government is subject to the Agreement with SAS Institute and the restrictions set forth in FAR , Commercial Computer Software-Restricted Rights (June 1987). SAS Institute Inc., SAS Campus Drive, Cary, North Carolina JMP, SAS and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute Inc. in the USA and other countries. indicates USA registration. Other brand and product names are registered trademarks or trademarks of their respective companies.

3 Release Notes for JMP Genomics This document describes changes and enhancements from JMP Genomics to The updates are available only via web download from You must first install JMP Genomics from CD media before running the updater. See the notes at the end of this document for detailed instructions on incorporating customized menus into JMP Genomics Beginning with this release, JMP Genetics, JMP Microarray and JMP Proteomics are now combined into a single JMP Genomics product. The updater enhances functionality in all three domains and fixes several minor bugs. New and improved features in JMP Genomics Analytical Processes (APs) are described in the following sections, and are organized according to the JMP Genomics main menu. Data Set Creation Affymetrix SNP CHP Import Engine The SNP columns are now automatically reordered so as to match the order of SNPs in the annotation data set. Illumina SNP Import Engine This is a new AP. The JMP.JMPCMD menu file has been updated to include this AP. A link to Illumina homepage has been added to the JMP Genomics Web Links help page. HapMap Import Engine This is a new AP. The JMP.JMPCMD menu file has been updated to include this AP. A link to the HapMap website as been added to the JMP Genomics Web Links help page. Bioconductor Expresso for Affymetrix The gcrma method has been added as an option for Background Correction. Log transformation is deactivated when the medianpolish option for expression summary is selected. Import Single Text, CSV, or Excel File A Data Step parameter field has been added to allow specification of SAS syntax to modify the Output Data Set.

4 Release Notes for JMP Genomics Import Multiple Text, CSV, or Excel Files Data Set Utilities A variable named Response is now recognized as an alias for Intensity in the Experimental Design File, and these variables can now optionally be character instead of numeric. Column Contents Reorder New options have been added to process only the first n columns, with n specified by the user. An option to remove columns not listed in the Column Order data set has been added. Transpose Tall and Wide A field allowing users to specify a list-style of variables to be transposed has been added to the Wide Tall tab. Applicable list-styles include variables that are numbered sequentially or contain a common prefix. Genetic Marker Statistics Phenotype Summary Additional marker statistics are provided for quantitative variables, including number of observations with missing values. Marker Properties Cell plot and frequency charts now function properly where there are markers with missing alleles or markers with fewer than three genotypes. Linkage Disequilibrium Missing p-values in the LD p-value plot are now represented by a distinct color. LD tagsnp Selection Numeric results have been corrected. An option for calculating maximum distance has been added. An option for specifying the method for Haplotype Estimation has been added.

5 Release Notes for JMP Genomics Association Testing Marker-Trait Association Variable names in the output are more descriptive than previously. Binary traits no longer must be defined by 0 and 1. TDT X-linked markers can now be identified using a clause that is applied to the annotation data set. Haplotype Analysis Haplotype Trend Regression Minor changes have been made to the interface. A variable selector for the Frequency variable from the Haplotype Frequency Data Set has been added. Results using a survival trait are now correct. Estimates and tests for the category of Rare haplotypes is now included in the output. Multiple Genetic Processes Marker variables containing genotypes like "AB" e.g. (with no delimiter) can now be used when %str() is given for the Genotype Delimiter option. Quality Control Data Distribution The way box plots are computed has been enhanced for performance. The new box plots are approximations based on the output from SAS PROC KDE. Correlation and Principal Components On the Variance Components tab, sliders were added for the first and last principal component to compute, and the default first component was changed from 1 to 2. The first principal component almost always associated with the overall mean values and is typically subtracted away. Pattern Discovery Multidimensional Scaling List-style specification of distance variables has been added.

6 Release Notes for JMP Genomics Row-by-Row Modeling One-way ANOVA ANOVA This is a new AP that fits one-way ANOVA models along with an optional random blocking effect. It runs much faster than ANOVA and Mixed Model Analysis because calculations are performed directly in a SAS data step. The JMP.JMPCMD menu file has been updated to include this AP. Minor interface enhancements and small bug fixes have been added. The output variable RSquared has been renamed to RSquare. Mixed Model Analysis Predictive Modeling Minor interface enhancements and small bug fixes have been added. The output variable RSquared has been renamed to RSquare. The MODEL statement option HTYPE=1,2,3 can now be handled. An error in reducing the number of records in the MMEI output has been fixed. Discriminant Analysis, K-Nearest Neighbors, Logistic Regression A performance enhancement for the genetic algorithm has been added.

7 Release Notes for JMP Genomics Menu Activation and Customization Following installation of this updater, you will need to activate the new JMP Genomics menu. Open JMP. Click Edit > Customize > Revert to Factory Defaults. Your JMP Menu customizations are saved in a text file called JMP.JMPCMD. During the activation process, the previous JMP.JMPCMD file, which includes any menu customizations you may have made previously, will be saved as JMP Backup Menu (date).jmpcmd. To incorporate customized menus into JMP Genomics 2.0.3, complete the following steps. Close all JMP sessions. Navigate to the folder containing your JMP.JMPCMD and backup files. These files are typically located in: C:\Documents and Settings\<userid>\Local Settings\Application Data\JMP6 Data\English\ Here <userid> is your personal local folder, typically similar to your login name. Note :The Local Settings file is typically hidden by default, so you will need to change your folder options to allow you to view hidden files. On Windows XP machines this is accomplished by clicking Tools > Folder Options > View > Hidden Files and Folders and selecting the Show Hidden Files and Folders option. Open each of the two JMP.JMPCMD files with a text editor. Compare the JMP.JMPCMD file with the backup file to identify custom menu items. Copy and paste desired menu items from the backup file into the JMP.JMPCMD file. Save and close the JMP.JMPCMD file. Open JMP and verify the menu changes.