Estimate Plots (IM and CIM Analysis)

The Estimate Plots tab is shown below:

The Volcano Plots tab contains the following elements:

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A Volcano Plot for each quantitative trait.

The volcano plot(s) show the LOD score for each trait plotted on the y-axis versus either the Estimate of the Additive Effect on the x-axis or the Estimate of the Dominance Effect (coded in reference to the effect of the parental line 2 or P2 allele). Each point on the plot represents a QTL testing location, with points colored by the chromosome or linkage group. Negative estimates indicate that there was a decrease in the quantitative trait associated with the allele from parental line 2. The black horizontal line represents a LOD threshold that was either specified on the process dialog or determined using permutation testing. Points to the upper left or upper right indicate locations with increasing evidence of a significant QTL that have large negative or positive effect on the trait of interest.

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One Data Filter.

The JMP Data Filter has also been embedded into this tabbed view to use for interactively selecting points in the plots.