List of Figures

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Figure 1. Overview of MAExplorer
Figure 1.1.1 Overview of MAExplorer exploratory data analysis system
Figure 1.1.2 Overview of data preparation for quantified spot data used by MAExplorer
Figure 1.1.3 Overview of running MAExplorer as a stand-alone application
Figure 1.1.4 Overview of running MAExplorer as a Web browser applet
Figure 1.3 Data Filter Venn diagram
Figure 1.4 Screen view of MAExplorer main window with Analysis Menu
Figure 1.5.1 The MicroArray Explorer home page
Figure 2.1.1 Example of the "Open file DB" command
Figure 2.1.2 Example of the "SaveAs file DB" command
Figure 2.2.1 Samples menu - setting lists of samples by using the "chooser"
Figure 2.2.2 Samples menu - selecting samples by source characteristics
Figure 2.2.3 Changing the current sample to either the HP-X or HP-Y sample
Figure 2.2.4 Samples menu - selectively swapping (Cy3,Cy5) data channels for particular samples
Figure 2.2.5 Popup condition chooser session
Figure 2.2.6 Popup ordered condition list (OCL) chooser session
Figure 2.3.1 Edited Gene List defined from Guesser using wildcards
Figure 2.3.2 Selection of gene sets for binary gene set operations
Figure 2.3.4.1 Popup window to adjust all threshold slider values
Figure 2.3.4.2 Dialog query to change HP-X Condition set name
Figure 2.4.2.3 Different normalizations to improve the "view"
Figure 2.4.3.1 Filtering using multiple scrollers
Figure 2.4.1.1 Gene Class menu
Figure 2.4.1.2 Gene Class 'replicate' genes occurring more than once in an array
Figure 2.4.3 Filter menu
Figure 2.4.4 Plot menu - selecting Ratio Pseudoarray image
Figure 2.4.4.1.1.1 Pseudoarray image intensity array with median normalization
Figure 2.4.4.1.1.2 Pseudoarray image intensity array with Zscore normalization
Figure 2.4.4.1.1.3 Pseudoarray image intensity array with Zscore Log normalization
Figure 2.4.4.1.1.4 Pseudoarray image intensity array with median norm. of dual HP-X & HP-Y
Figure 2.4.4.1.1.5 Pseudoarray image intensity array with median norm. of dual HP-X & HP-Y 'sets'
Figure 2.4.4.1.2.1 Pseudoarray image of X/Y ratio with median data normalization
Figure 2.4.4.1.2.2 Pseudoarray image of X/Y 'sets' ratio with median data normalization
Figure 2.4.4.1.2.3 Pseudoarray image of X-Y Zdiff data normalization
Figure 2.4.4.1.2.4 Pseudoarray image of X-Y 'sets' Zdiff of log data normalization
Figure 2.4.4.1.2.5 Pseudoarray image color-coded pValue for t-test of HP-X & HP-Y 'set's
Figure 2.4.4.2 Scatter plot of HP-X and HP-Y single sample data
Figure 2.4.4.2.1 Scatter plot of HP-X and HP-Y single sample data
Figure 2.4.4.3 Histogram plots
Figure 2.4.4.4 Expression profile plots
Figure 2.4.4.4.1 Expression profile plots
Figure 2.4.5 Cluster menu options
Figure 2.4.5.1 Cluster of genes similar to current gene
Figure 2.4.5.2 Display of cluster counts
Figure 2.4.5.3 N-Primary-Node cluster method
Figure 2.4.5.4 Hierarchical clustering clustergram
Figure 2.4.6.1 Sample Reports windows
Figure 2.4.6.2 Gene Reports windows
Figure 2.5 View Menu
Figure 2.5.1 Popup Unigene browser database page
Figure 2.5.2 Examples of messages and command history popup log windows
Figure 2.6 MAEPlugins paradigm
Figure 2.6.1 Loading a MAEPlugin from your file system
Figure 2.6.2 Executing a command previously loaded in Plugin menu
Figure 2.6.3 Popup window from executing the MAEPlugin
Figure 2.7 Help Menu
Figure 4.4 Dryrot error message window
Figure 4.4.1 Dryrot error after SaveAs window
Figure C.1 Directory structure of stand-alone DBs required by MAExplorer
Figure C.6.1The Cvt2Mae array data converter
Figure D.1 Installing MAExplorer a stand-alone application
Figure E.4.1 Overall MAEPlugin design for MAExplorer
Figure E.4.2 Open Java API for MAEPlugins showing the specialized Java classes