QTL Single Marker Analysis

Running this process using the F2sample sample setting generates the tabbed Results window shown below. Refer to the QTL Single Marker Analysis process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

•	Summary Chart: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for each test.

Note: The Summary Chart tab will not be shown if the Chromosome field is not specified in the Annotation tab.

•	Manhattan Plot: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays a scatter plot of the p-values across all annotation groups colored by annotation group.

•	All P-Value Plots: When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the p-value plots from the Annotation Group Results tabs in a single display.

Note: When an annotation group variable is not specified, as in this example, or there is only one annotation group, the tab is named P-Value Plot and contains an overlay plot of p-value by chromosome location for all markers.

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Volcano Plot(s) (QTL Single Marker Analysis): This tab displays a scatter plot of p-values by the Estimate of P2 Allele Genotype Effect for all markers, colored by annotation group (chromosomes or genes, for example). Estimate of P2 Allele Genotype Effect is the estimate of regression slope for the numeric marker genotype treated as a continuous variable.

Drill Down Buttons

Action buttons provide you with an easy way to drill down into your data. The following action buttons are generated by this process:

•	Trend: Surfaces a Venn diagram of significant markers by trait variables. This is useful for the visualization of overlapping significant markers across Trait Variables.

Output Data

This process generates the following data sets:

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Trend Parameter Estimate Output Data Set: This data set contains the estimates and test statistics for the fixed effects of any Co-factor Variables included in the regression model and the numeric marker genotype treated as a continuous variable. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _pet. Click Open to view the data set.

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P-Value Output Data Set: This data set contains all the columns from the annotation data set, plus the test statistics and p-values from the tests performed. This data set can be used as the annotation data set for subsequent processes to accumulate results from multiple processes into a single data set. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _sma. Click Open to view the data set.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

General

•	Click View Data to reveal the underlying data table associated with the current tab.

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.