geWorkbench

geWorkBench Component List and Status

Core Components (bundled with main application)

Major Components

• Analysis (Hierarchical Clustering, SOM, T-Test, Multi T-Test)
• Filtering (Deviation, Affy detection call, Expression threshold, Genepix Flags, Missing values, 2 channel)
• Normalization (Housekeeping, Log2 transform, Marker based centering, Mean variance, Array based centering, Missing value, Threshold, Quantile)
• Expression Value Distribution
• Go Terms
• Reverse Engineering (should perhaps be broken into seperate components)
• Scatter Plot
• Tabular microarray
• Sequence retriever

Minor Components

• Dataset Annotation
• Dataset history
• Experiment info

Components that do not yet pass the Plugin certification checklist

• Associations (Interface needs to be standardized)
• caScript (Not yet complete)
• Synteny parameters (Does not generate proper dataset subnodes)
• Synteny main paen (Does not receive proper dataset subnodes, function not clear)
• Marker Annotations ("Retrieve Annotations" button should be disabled until user makes marker selection)
• Color Mosaic ("Pat" and "Abs" buttons appear to do nothing)
• Expression Profiles (Performs large computations on event reception and tab selection)
• caBIO Pathways (Function not tied properly to datasets, operation not clear)