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
One-Way ANOVA
process description for more information.
Click
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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Variability Estimates
: This tab shows the analyses on
variance
component estimates from the
ANOVA
model fits.
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Standardized Residual Plots
: This tab shows the analyses on
residual
from the
anova
model fits when you have requested them in the
dialog
.
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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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SAS Output
: This is a text-based output directly from SAS PROC UNIVARIATE. Refer to the documentation for
SAS PROC UNIVARIATE
for more information.
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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 results
1
satisfying
all
of the cutoff criteria specified (
Mean Difference Filter Cutoff
,
Direction of the Cutoff
, and
-log
10
(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
: This output data set 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 generate a
pdf
- or
rtf
-formatted report containing the plots and charts of selected tabs.
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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.