RAMA - Robust Analysis of Microarray

Rama Initialization Dialog


Rama

Rama is an intensity normalization algorithm based on hierarchical Bayesian modeling. Rama has been designed to work with raw intensities ( Affymetrix or 2 color ), especially in dye-swap experimental designs. It estimates intensities and as such requires there to be at least 2 data points for each color label.

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. Rama 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 Rama

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 RAMA. 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.