Difference between revisions of "Preferences"

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==Introduction==
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The Preferences item in the menu bar allows a number of features of geWorkbench to be configured.
  
 
[[Image:Menu_Bar_Preferences.png]]
 
[[Image:Menu_Bar_Preferences.png]]

Revision as of 16:15, 25 May 2011

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot


Introduction

The Preferences item in the menu bar allows a number of features of geWorkbench to be configured.

Menu Bar Preferences.png


Text Editor

The user can change the default text editor used to view data files. For example, when you right-click on a data node in the Project Folders component, "View in Editor" is one of the options offered.


Visualization

Heat maps, e.g. in the Color Mosaic component, can be displayed using either a relative or an absolute color scheme.

Note - Changing the relative/absolute preference will not take effect until the next time a data set is loaded.

  • Absolute
    • Red represents positive expression values, and green represents negative expression values. Black represents a value of zero. The shade represents the expression magnitude as follows:
    • Formal spec: Let M = max{|min|, |max|} over all expression measurements, across all arrays. If expression value x > 0, assign it the red spectrum x / M * 256. If expression value x is negative, assign it to the green spectrum -x / M * 256.
  • Relative (default)
    • Relative is similar to the setting for Absolute, but each marker is mean-variance normalized first. A Red-Blue color scheme is used, with red representing the highest values and blue the lowest. White represents the marker average.
    • Note - Relative will give odd-looking results if only a small number of arrays are loaded.

GenePix Value Computation

Four methods for calculating a composite expression measurement for each marker in a GenePix file are offered. They combine the foreground and background and mean or median measurements from each channel in different ways.

  1. ( F635 Mean - B635 Mean) / (F532 Mean - B532 Mean).
  2. ( F635 Median - B635 Median) / (F532 Median - B532 Median).
  3. ( F532 Mean - B532 Mean) / (F635 Mean - B635 Mean).
  4. ( F532 Median - B532 Median) / (F635 Median - B635 Median).

See the entry GenePix Format in the GenePix tutorial chapter for further details of processing GenePix data on input.

Remote Components URL

geWorkbench can download certain components from a network repository. This specifies the location of the network component repository.