RMSE (Build Consensus Linkage Map)

The RMSE tab is shown below:

The RMSE tab contains the following elements:

•

Oneway Analysis of Root Mean Square Error By Maximum Interval Window Linkage Group= Z.

This plot displays the root mean square error (RMSE) (y-axis) versus maximum interval window values (x-axis) for input linkage group Z (where Z is the input chromosome name). Each colored filled-circle represents the RMSE for a given input linkage map.

Note: There is a separate plot for each input linkage group.

This plot can be used to determine the optimal value for the maximum interval window to use in building a consensus map because the smaller the value of the RMSE, the better the consensus map fits the input map. IN addition, the smaller the RMSE, the better the consensus map fits all of the input maps.

In the example shown here, a maximum interval of 2 leads to the best fit of the consensus map to the six input linkage maps.