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YMD > Data Analysis

• Commercial analysis software available through Keck workstations:
  • QuantArray software for microarray image analysis is available on one workstation in LH203 and two public workstations in SHM IE53. Quantarray reads (GSI Lumonics) .tif images and quantifies florescent channel intensities for each gene. Descriptive statistics and simple data plots can be produced from the intensity values. Raw intensity data can be saved as a tab-delimited text file suitable for further analysis. (See procedure for access to workstation at the Keck DNA Microarray Core Laboratory).
  • Axon GenePix analysis software is available on LH203 and SHM IE53 workstations. View a GenePix PowerPoint Tutorial

• Custom tools available at Mark Gerstein's Lab:  
  • A tool for ranking protein domains in terms of expression levels

• Custom tools available at Hongyu Zhao's software download site: http://bioinformatics.med.yale.edu
  • QAnalyzer 1.0 statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
  • QAmerge 1.0e Pooling replicated microarray datasets exported from QuantArray image analysis software.
  • QAnalyzer 1.0 Statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
  • GPmerge 4.0b Pooling replicated microarray datasets exported from GenePix Pro image analysis software.
  • GProcesser 1.0 statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.
  • GProcesser 2.0 ^NEW! Statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.

• Academic software and resources available from other sites:
  • ScanAlyze PC based software, available by downloading from Mike Eisen at http://rana.lbl.gov/
  • Cluster PC based software, available by downloading from Mike Eisen at http://rana.lbl.gov/
  • Treeview PC based software, available by downloading from Mike Eisen at http://rana.lbl.gov/
  • J-Express a freeware available at http://www.ii.uib.no/~bjarted/jexpress/install.html
  • SOURCE, the Stanford Online Universal Resource for Clones and ESTs compiles information from several publicly accessible databases, including UniGene, dbEST, SwissProt, GeneMap99, RHdb, GeneCards, and LocusLink. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene.

Copyright © 2003, Yale University, New Haven, Connecticut, USA. All rights reserved.
Comments or suggestions to Greg Blasko.

Last modified: 28-Mar-2003 (GB)