IDEA
IDEA
Notes
Networks read in from files into the geWorkbench Project Folders component can be represented as Entrez ID, gene symbol, or probeset id. However, geWorkbench currently converts Entrez ID networks to gene symbols.
The IDEA analysis, for compatibility with its grid service implementation, first converts each network node, in case it is represented a gene symbol or probeset id, to an Entrez ID. In case multiple nodes map to the same Entrez ID, they are combined. In the case that a probeset is annotated to more than one Entrez ID, it is expanded to multiple nodes.
The network can be loaded from the Project, or loaded directly from file in ADJ or SIF format.
If the network contains nodes that are not found in the current microarray data set, a warning pop-up appears.
Network conversion to Entrez IDs is carried out after the "Analyze" button is pushed.
The mutual information parameter settings are apparently fixed, no preprocessing is available.
Only genes with a NES > 0 are included in the results table.
