MAExplorer Newsletter #4, October 17, 2001 ========================================== This newsletter is issued periodically to announce major changes and enhancements to the MicroArray Explorer (MAExplorer). Since you have expressed an interest in MAExplorer in the sypast, you were included in this newsletter mailing. If you don't wish to receive further mailings, let us know and we will remove you from the list. Old newsletters are available in the Web site archive, so if you are interested in following developments in MAExplorer but don't want the E-mail you could get the information there. WEB SITE: http://www.lecb.ncifcrf.gov/MAExplorer CONTACT: mae@ncifcrf.gov PHONE: 301-846-5535 (Peter Lemkin) 301-846-5539 (Greg Thornwall) FAX: 301-846-5598 NEWSLETTER ARCHIVE: http://www.lecb.ncifcrf.gov/MAExplorer/Newsletters/ Enhancements in the current Version 0.92.09 since the last Newsletter ===================================================================== At the time of the last August 20, 2001 newsletter #3, the version was 0.90.08. There were a number of improvements and new features added as well as the Beta-release of a data format conversion tool (Cvt2Mae). Details on these features are described in the Reference Manual. 1. A New Download installer is being used for distributing MAExplorer --------------------------------------------------------------------- MAExplorer is now distributed with InstallAnywhere 4.5 (previous was version 4.0.1). This now supports MacOS-X, other unix systems and may fix some other installation problems. 2. A number of new gene data filters have been added ---------------------------------------------------- 2.1 The data filter "Filter by 'Good Genes List' membership" was renamed to "Filter by global 'Good Genes List' membership". This filter uses QualCheck data in the GIPO print file (GAL file). 2.2 The data filter "Filter by 'Good Spot data'" was renamed to "Filter by per-sample 'Good Spot data'". This users per-sample hybridization good spot data using the QualCheck data in the spot quantification (.quant) files. 3. New pseudo array image mode ------------------------------ A new pseudo image array display has been added a "Pseudocolor Red-Yellow-Green Cy3/Cy5 ratio or Zdiff". This displays the Cy3 and Cy5 microarrays as a pseudocolor image. The the Cy3 (red) and Cy5 (green) components are added together so that high total intensity values are yellow and low values are black. High Cy3/Cy5 ratio values are more red and low values are more green. Note: this is only available with Cy3, Cy5 ratio data. 4. The Cvt2Mae data format conversion tool ------------------------------------------ A Java stand-alone Cvt2Mae data format conversion tool is being beta-tested. This tool lets the user convert their array data to MAExplorer format so it may be used with MAExplorer. This is described in the Reference Manual Appendix C.6 and the Cvt2Mae home page (http://www.lecb.ncifcrf.gov/Cvt2Mae) where you may download the converter to your computer. It currently handles Incyte and Affymetrix layouts (beta-testing). It is being generalized to allow users to define and save their own array layouts for their own special arrays or array data. Check the Cvt2Mae Web page to find the latest status of new features. The Cvt2Mae Affymetrix mode now generates Good Spot data based on "Abs call" data in the Affy data file. MAExplorer has been modified to handle Affymetrix (or other) data converted with Cvt2Mae when there is no genomic "Identifier" field. In that case, "Location" is used as the genomic identifier. 5. Fixed problem with saving indicated swapped (Cy5/Cy3) samples ---------------------------------------------------------------- Fixed a bug in "Edit use (Cy5/Cy3) else (Cy3/Cy5) for each HP" for use with ratio data. The previous version did no always save the swap changes. This command lets selectively swap (Cy3,Cy5) data entries so they may use (carefully!) additional dye-swap data samples for use as replicate samples. 6. Documentation ---------------- 9.1 The Reference Manual and tutorials have been clarified and revised and new material added. 9.2 The Web page devoted to MAExplorer PDF (Adobe Acrobat) documents has been updated. 9.3 A Web page for MAExplorer plugins has been added http://www.lecb.ncifcrf.gov/MAEPlugins). Additional documentation on plugins will appear here. Future enhancements under development ===================================== * Added functionality in the Cvt2Mae data format conversion tool for "User-defined" data. * User extensible analysis methods using Java Plugins by having users write to a MAExplorer Java plugin API (check for status on the web page http://www.lecb.ncifcrf.gov/MAEPlugins) * New data filtering methods * New normalization methods * New clustering methods * Improved graphics * Improved documentation and training films * Access additional genomic Web databases * Generation of extracted image spot regions for specific genes across a set of samples * etc. Please contact us with your comments, suggestions and problems in running MAExplorer at mae@ncifcrf.gov.