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.
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.
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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.
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Note
: The
Summary Chart
tab will not be shown if the
Chromosome
field is not specified in the
Annotation
tab.
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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.
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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.
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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.
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: Surfaces a
Venn diagram
of significant markers by
trait
variables. This is useful for the visualization of overlapping significant markers across Trait Variables.
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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
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
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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