Difference between revisions of "Preferences"

(Introduction)
Line 4: Line 4:
 
The Preferences item in the menu bar allows a number of features of geWorkbench to be configured.
 
The Preferences item in the menu bar allows a number of features of geWorkbench to be configured.
  
[[Image:Menu_Bar_Preferences.png]]
+
[[Image:Preferences.png]]
 
 
  
 
==Text Editor==
 
==Text Editor==

Revision as of 17:59, 31 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.

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.