BRIDGE - Bayesion Robust Inference of Differential Gene Expression
Bridge Initialization Dialog
Bridge
The bridge package consists of several functions for testing for differential expression
among multiple samples.
Data Type
The type of data that was loaded
If the data is affy, but was not loaded through the affy loader, choose "Intensity Data". This is
allows users to export Affy data from GCOS or GCRMA as text files and load them into MeV.
Experiment Labeling
Each slide (experiment or hyb) loaded into MeV is listed here. You must tell Rama how you've
labeled your samples.
If you've loaded 2 color data, you are asked to indicate which color ( Cy3 or Cy5 ) dye was
used on your control samples. It is assumed that the other was used for the treated sample
on that slide. Bridge will infer from the labeling whether or not your experiment was dye-swapped
based on your input here. Keep in mind that Rama requires at least 2 of any color data.
Advanced Parameters
# Iterations ( B ) - the number of iterations used by Bridge
Burn In Period ( num.iter ) - the length of the burn-in period in the MCMC algorithm. This
should be less than # Iterations ( B )
Rserve
This implementation has been built allow the user to connect to any Rserve daemon. Upon
load, the pull down menu is populated with the connection strings from the config file
( config/tmev.cfg ). The user can add a new connection string here if desired.
The format is: ipaddress:port.
For example, if the server running Rserve is at IP address 192.168.0.1 and
Rserve is running on its default port ( 6311 ), the connection string would be 192.168.0.1:6311.
The user can type that into the text field, click add, make sure it is selected in the pull down
menu and then run Bridge. If the connection was made without any errors, the new connection
string will be added automatically to the config file. Of course, the user always has the option
of manually adding/editing the connection strings in the config file.
See http://www.expression.washington.edu/ramaDoc/MeV-R_Documentation.html for more details