TDT

Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the TDT 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.

The Results window contains the following panes:

Tabs

This pane enables you to access and view the output plots and associated data sets on each tab. Use the drop-down menu to view the tab in the Tab Viewer pane, open the tab in a new window, or remove the tab and its contents from the Tab Viewer pane.

The following tabs are generated by this process:

•	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. Separate bar charts are shown for each BY group when any BY variables are specified. This tab is open by default.

•	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.

•

Annotation Group Results: When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab with an overlay plot of p-value by chromosome location is created for each annotation group. If the Calculate trend odds ratios check box was checked, this tab also contains a Volcano Plot of p-value by log odds ratio for all markers.

In this example, there are two annotation groups (CandGene 1, and CandGene 2) and, thus two Annotation Group Results tabs (CandGene 1 Results and CandGene 2 Results).

•	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 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.

•	Cell Plot: When the Display cell plot of Mendelian errors check box has been checked, this tab displays a cell plot of Markers by Pedigree, colored by presence or absence of an error.

Drill Downs

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

•	Create Subset Genotype and Annotation Data Sets: Select points from the p-value plots and click Create Subset Genotype and Annotation Data Sets to open the Subset and Reorder Genetic Data process to create the subset data sets.

Note: This action button is not available if any By Variables are selected.

•	GenBank Nucleotide: Select points or rows and click GenBank Nucleotide to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.

•	UniGene Database: Select points or rows and click UniGene Database to access information from the Unigene database for selected genes or markers

•	AceView Database: Select points or rows and click AceView Database to access information from the ACEView database for selected genes or markers.

•	dbSNP: Select points or rows and click dbSNP to open a browser window directed to an NCBI dbSNP search for the pair of SNPs associated with the particular instance of this button.

Output Data

This process generates the following data set(s):

•

P-value 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 _tdt. Click Open to view the data set.

•

Allelic Transmissions Data Set: This data set contains the columns from the input data set merged with the pair of allelic transmission scores, the between or expected genotype in the B_ columns and the within or genotype deviations in the W_ columns, for each individual at each marker allele. This information can be used to determine counts of transmitted and untransmitted alleles. Click Open to view the data set.

This data set is generated when the Create output data set containing allelic transmissions check box has been checked.

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

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window.

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.