Running this process using the XTitrationExample sample setting generates a JMP journal (shown below) containing links to the chromosome-specific analysis results as well as to the combined results. Refer to the Bivariate One-Way ANOVA process description for more information.
Click , on the ANOVA Differences journal to open the tabbed Results window shown below. 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.
Note: Each of the tabbed Results windows for the analysis can be accessed from the Journal. All of these windows are similar to the one shown here.
The Results window contains the following panes:
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.
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Results: This tab shows the primary results from the analysis, including volcano plots and various analyses on least squares means.
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Ave Sig Index Chromosome Plots: This tab plots the proportion of the observed differences that are statistically significant by position on the specified chromosome.
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Chromosome Position Plots: This tab shows a separate overlay plot for each chromosome of the meta-analysis p-value by chromosome location for the markers This tab is generated whenever a Chromosome Variable is specified.
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Variability Estimates: This tab shows the analyses on variance component estimates from the anova model fits.
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IPA Upload: Select points or rows and click to open the IPA Upload process with the selected points specified as input data.
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UCSC Genome Browser: Select points or rows and click to open the UCSC Genome Browser process with the selected points specified as input data.
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Annotation Summary: Select points or rows and click to summarize annotation information for the selected genes or markers
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GO Stat: Select points or rows and click to access, annotate, and analyze information for selected molecular entities in the Gene Ontology database.
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Onto-Express: Select points or rows and click to retrieve annotation information for selected gene or markers from the Onto-Express database
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GenBank Nucleotide: Select points or rows and click to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.
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UniGene Database: Select points or rows and click to open a browser window directed to a UniGene Database search for the selected molecular entities.
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AceView Database: Select points or rows and click to access information from the ACEView database for selected genes or markers.
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Open Subset in Tall Format: Select points or rows and click to create a tall version of the input data for the selected genes.
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Open Subset in Wide Format: Select points or rows and click to create a wide version of the input data for the selected genes.
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Fit Model and Plot LS Means: Select points or rows and click to select variable(s) that uniquely define wide column names. Selected genes are analyzed in the JMP Fit Model platform to view detailed fitting results and plots.
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Attention: Read the warning found in the link.
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Construct One-way Plots: Click to plot the original data in one-way format using treatment variables of your choice.
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Launch Plot Intensities: Select points or rows and click to launch the Plot Intensities process on the selected genes.
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Venn Diagram: Click to launch an open dialog from which you can select up to 5 comparisons and create a Venn diagram to display the overlap of significant genes from those comparisons.
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Launch JMP Genomics Browser: Select points or rows and click to launch the JMP Genomics Browser process for the selected points.
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Create Subset with Mean Difference and P-value Criteria: Optionally select points in a graph. Click to create custom subsets based on mean differences and/or p-value cut offs that you specify in a window that appears after you click this action button. Each l probe with at least one of the results1 satisfying all of the cutoff criteria specified (Mean Difference Filter Cutoff, Direction of the Cutoff, and -log10(p-value) Cutoff fields) is placed in the subset data set.
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Note: This button is not surfaced unless LSMeans Effects are specified.
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Enter new -log10(p) cutoff: Enter a new value in the text box to change the horizontal dashed red line in the volcano plots that is used for determining statistical significance. Click to update all plots to reflect the new cutoff.
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Significant Differences Data Set: These output data sets contains a complete list of the genes significant by one or more criteria. This data set is indicated by the _sig suffix. Click to view the data set.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
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Click to reveal the underlying data table associated with the current tab.
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Click to reopen the completed process dialog used to generate this output.
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Click to close all graphics windows and underlying data sets associated with the output.
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Specified using the Select One or More Mean Difference Columns field in the window that appears after you click this action button.