Difference between revisions of "Information Panel"

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(Information Panel: Dataset History, Annotation and Experiment Information)
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[[Image:Information_Panel.png]]
 
[[Image:Information_Panel.png]]
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Note - prior to geWorkbench v2.3.0, these three windows appeared as separate tabs in the geWorkbench Commands area.
  
 
===Dataset History===
 
===Dataset History===
The Dataset History component is used to log the data transformations applied by operations such as the application of filters, normalizers, etc. For example, when a dataset in the Project Folders is normalized, the Dataset History for that dataset is updated to record that event. Dataset histories are part of the workspace and are persisted when the workspace is saved with their pertinent dataset. Data in the Dataset History pane is non-editable.
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The Dataset History window logs the settings used for analysis, filtering and normalization. Dataset histories are part of the workspace and are persisted when the workspace is saved. Data in the Dataset History pane is non-editable.
  
  
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===Experiment Information===
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===Experiment Info===
 
Experiment Info is a non-editable component intended for viewing information associated with a Microarray dataset. What constitutes "experiment information" varies depending on the source of the microarray dataset.  E.g., for Affymetrix MAS5 files the file preamble (the part just before the data lines which provides various experiment execution parameters) becomes the experiment information.
 
Experiment Info is a non-editable component intended for viewing information associated with a Microarray dataset. What constitutes "experiment information" varies depending on the source of the microarray dataset.  E.g., for Affymetrix MAS5 files the file preamble (the part just before the data lines which provides various experiment execution parameters) becomes the experiment information.
  

Revision as of 15:19, 1 March 2012

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



Overview

geWorkbench provides several mechanisms by which descriptive information about particular data nodes can be viewed and added. These include "hover text" in the Project Folders component for certain dataset types, and several text windows for different types of information. These later components are displayed in the Command and Analysis area of geWorkbench.

Project Folders Component

For microarray datasets, adjacency matrices (network nodes), sequence and pattern nodes, moving the mouse cursor over the data nodes will display additional details about a dataset.

Microarray datasets: hover text displays number of markers and arrays.


Dataset hover microarray.png


Adjacency Matrix: hover text displays number of nodes and edges in the network.


Dataset hover network.png


Sequence node:


Dataset hover sequences.png


Pattern node:


Project Folders Pattern Hover.png

Information Panel: Dataset History, Annotation and Experiment Information

After any operation on a data node, such as analysis, normalization, or filtering, certain information is stored to that data node's Information Panel. The Information Panel is divided into three sub-windows.


Information Panel.png


Note - prior to geWorkbench v2.3.0, these three windows appeared as separate tabs in the geWorkbench Commands area.

Dataset History

The Dataset History window logs the settings used for analysis, filtering and normalization. Dataset histories are part of the workspace and are persisted when the workspace is saved. Data in the Dataset History pane is non-editable.


Dataset Annotation

The Dataset Annotation component allows users to attach comments to Project Folders nodes. A user first selects the node of interest in the Project Folders tree and then enters the desired annotation (in the form of free text) in the Dataset Annotation pane. Annotations are stored along with their corresponding Project Folder nodes when the workspace is saved.


Experiment Info

Experiment Info is a non-editable component intended for viewing information associated with a Microarray dataset. What constitutes "experiment information" varies depending on the source of the microarray dataset. E.g., for Affymetrix MAS5 files the file preamble (the part just before the data lines which provides various experiment execution parameters) becomes the experiment information.

Currently only header information from GEO files appears to be supported.

Experiment Info GEO.png