RELEASE NOTES for ArrayAnalyzer 2.1.1 ===================================== ArrayAnalyzer 2.1.1 is a new release for use with S-PLUS 7.0. The first section of these release notes describe the changes (Enhancements and Bug Fixes) from ArrayAnalyzer 2.0.1 to ArrayAnalyzer 2.1.1. The original release notes for ArrayAnalyzer 2.0.1 are included in the second section. Enhancements Included in ArrayAnalyzer 2.1.1 -------------------------------------------- LPEtest library resampling option has been speed up. Help pages for dialogs now load much faster. just.gcrma and just.rma functions were added and optimized. These allow reading in an summarizing more than 200 CEL files on a high-performance desktop computer. In the ANOVA dialog, for 2-channel reference design, you now can select whether to analyze M (differences) or A (averages). The ANOVA dialog allows one and two-way analysis of datasets with more than 2 factors, new dialog controls allow you to select which factors to include in the model. When doing hierarchical clustering from the dialog you now have the option to choose a colorscheme for image plot. The surface method used for the loess smooth in maLoess was changed from "direct" to "interpolate". This makes loess normalization for two-channel data much faster. Support for reading GenePix Pro 6.0.0.45 files added. These files do not have the same column names so ArrayAnalyzer 2.0.1 would not import them. They can now be read from the Import Data From Two Channel dialog. The rma background correction when doing Mix & Match on the Affymetrix Expression Summary dialog is now using the RMA Version 2 algorithm (bg.correct.rma2). This is the same background correction algorithm that the composite RMA and GCRMA selections (also on the Affymetrix Expression Summary dialog) use. Bug Fixes Included in ArrayAnalyzer 2.1.1 ------------------------------------------ The gene list html output has the means rounded to 3 significant digits. The gene list output has better title and supporting info included. The parallel coordinates plots from the clustering dialog now have correct the x-axis labels instead of just numbers. When the Gene List Management dialog is running, the status dialog now says "performing gene list management" instead of "performing clustering ..." The MvA plots from the QC Diagnostics dialog for CEL data are now all on the log scale. A "None" option was added to the FDR adjustment options on the ANOVA dialog. The RNA degradation plot from the QC Diagnostics dialog now identifies the extreme chips. You can no longer do image plots for summarized Affymetrix data from the QC Diagnostics dialog. Image plots for this type of data are not appropriate. On the QC Diagnostics dialog you can now select which CEL file to create an image plot rather than drawing image plots for all the files. The boxplots created by the Affymetrix Summary dialog now note that the data is on the log2 scale. The show method for marrayNorm objects could fail if there are no missing values in the data. This has been fixed. lpeOLIG could fail if you tried to analyze a small number of genes and used the default values for the number of bins and smoother degrees of freedom. The default values are now adjusted when analyzing a small number of genes. Release Notes for S+ArrayAnalyzer Version 2.0 (June 2004) ========================================================= These Release Notes are current as of June 2004. For updates to the Release Notes that are made after this date and other useful information, please see the Web site www.insightful.com/support/ArrayAnalyzer ************************************************************************ Contents of these Release Notes ************************************************************************ * LICENSING * SUPPORTED PLATFORMS AND SYSTEM REQUIREMENTS * INSTALLATION INSTRUCTIONS * RUNNING S+ArrayAnalyzer * NEW FEATURES IN S+ArrayAnalyzer 2.0 * CONTACT INFORMATION FOR FEEDBACK ************************************************************************ LICENSING ************************************************************************ Insightful Corporation owns the S+ArrayAnalyzer software program and its documentation. Both the program and documentation are copyrighted with all rights reserved by Insightful Corporation. S+ArrayAnalyzer provides access to the Bioconductor R packages for microarray analysis, which are free software. The affy, annotate, Biobase, edd, gcrma, genefilter, geneplotter, LPEtest (provided by Insightful), marrayClasses, marrayInput, marrayNorm, marrayPlots, matchprobes, multtest, ROC, and vsn libraries are copyrighted © 2004 by Insightful Corporation. These libraries are free software that are redistributed and modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; version 2.1 of the License. The S+ArrayAnalyzer software is covered by a separate license agreement. ************************************************************************ SUPPORTED PLATFORMS AND SYSTEM REQUIREMENTS ************************************************************************ S+ArrayAnalyzer Version 2.0 requires S-PLUS 6.2 or later on Microsoft Windows. Windows Requirements S+ArrayAnalyzer 2.0 for Windows is supported on the following: Windows XP Professional Windows 2000 running on Intel platforms Windows 2003 Server The minimum recommended system configuration is a Pentium III/1Ghz with 1GB of RAM. You must have at least 850MB of free disk space for the typical installation. *********************************************************************** INSTALLATION INSTRUCTIONS *********************************************************************** Detailed information instructions are located at the top level of the S+ArrayAnalyzer CD-ROM. The file name is install_pro.txt or install_net.txt depending on the edition of S-PLUS (Professional or Windows Network) that you are using. ************************************************************************ RUNNING S+ArrayAnalyzer ************************************************************************ At the command line within S-PLUS, enter > module(ArrayAnalyzer) From the S-PLUS GUI menu, you can also load ArrayAnalyzer by selecting File > Load Module > ArrayAnalyzer ************************************************************************ NEW FEATURES IN S+ArrayAnalyzer 2.0 ************************************************************************ *Enhanced import for Affymetrix and two-channel microarray data including support for binary Affymetrix data files *Support for more than two level factors *Graphics for quality control and data diagnostics *Gene and array filtering *Differential expression testing with linear models (e.g., ANOVA, nested models) for time course and multi-factor designs *Cluster analysis including hierarchical and partioning methods available from a dialog *Annotation and gene list management available from a dialog ************************************************************************** CONTACT INFORMATION FOR FEEDBACK ************************************************************************** Please feel free to contact us with questions or feedback about this release. Send all technical support queries and general comments to one of the locations listed below. North, Central, and South America Contact Technical Support at Insightful Corporation: Telephone: 206.283.8802 or 1.800.569.0123, ext. 235 Monday-Friday, 6:00 a.m. PST (9:00 a.m. EST) to 5:00 p.m. PST (8:00 p.m. EST) E-mail: support@insightful.com Web: www.insightful.com/support Fax: 206.283.8691 All Other Locations Contact the UK office of Insightful Corporation: 5th Floor Network House Basing View Basingstoke, Hampshire RG21 4HG Tel: +44 (0) 1256 339800 Fax: +44 (0) 1256 339839 E-mail: shelp@insightful.com If you purchased ArrayAnalyzer through our international distributor network, contact your local distributor: http://www.insightful.com/contactus/internationaldistributor.asp We are very interested in receiving information on possible bugs and usability enhancements from all users. Bug reports can be sent to the following e-mail address: bugs@insightful.com