Summary Statistics

This report identifies unusual summary statistics across the entire study or by study visit (if requested). This analysis would typically be used on Findings tests representing continuous variables.

Note: JMP Clinical uses a special protocol for data including non-unique Findings test names. Refer to How does JMP Clinical handle non-unique Findings test names? for more information.

Report Results Description

Running this report with the Nicardipine sample setting generates the report shown below.

The Report contains the following elements:

Summary Statistics Volcano Plot

Shows a volcano plot used to determine the deviation of a mean or variance for Findings tests at a site versus other sites. Each point represents a single Findings test for a specific site. Here, the X axis represents the standardized difference in means between each between the site and the reference set (all other sites). For comparisons of variances, the X axis represents the log2(Ratio of Variances) between the site and the reference set.

This section can differ depending on the type of analysis that you perform.

Analysis of Mean or Variance

If you specify either Mean or Variance, you generate a volcano plot similar to that shown below:

This section contains the following elements:

•

One Data Filter.

Enables you to subset subjects based on country of origin, study site and/or Test. Refer to Data Filter for more information.

•

One Volcano Plot.

The volcano plot is used to determine the deviation of a mean or variance for Findings tests at a site versus other sites. Each point represents a single Findings test for a specific site. Here, the X axis represents the standardized difference in means between each between the site and the reference set (all other sites). For comparisons of variances, the X axis represents the log2(Ratio of Variances) between the site and the reference set. -log10 (p-values) are plotted on the Y axis. While most of the findings are close to the means across all of the sites. some of the points lie farther to the right or left of 0, indicating larger differences between the site and the reference set.

You can mouse over points of interest to see their labels or select points by dragging a mouse rectangle over them (as shown above). Selected rows are highlighted in other plots and you can also then click on various Drill Down Buttons for further analyses on those specific sites. In this example, we click to view summary statistics for the selected point skewed to the right. The corresponding row is viewed in the following subset.

The mean systolic blood pressure findings at this site average 13 points higher than the other sites. This finding might warrant further investigation.

Analysis of Skewness or Kurtosis

If you specify either Skewness or Kurtosis, you generate a volcano plot similar to that shown below:

This section contains the following elements:

•

One Data Filter.

Enables you to subset subjects based on country of origin, study site and/or Test. Refer to Data Filter for more information.

•

One Ratio plot.

This plot shows the ratio of skewness or kurtosis from site to reference, with bubbles size by # of measurements. Values far from 1 on the Y axis indicate large differences, which might warrant further exploration, though bubbles of small size (low sample size) might represent random noise.

Action Buttons

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

•

Show Summary Statistics: Shows the rows of the data table for the selected points from the volcano plot (see above)

General

•

Click

to view the associated data tables. Refer to View Data for more information.

•

Click

to generate a standardized pdf- or rtf-formatted report containing the plots and charts of selected sections.

•

Click

to generate a JMP Live report. Refer to Create Live Report for more information.

•

Click

to take notes, and store them in a central location. Refer to Add Notes for more information.

•

Click

to read user-generated notes. Refer to View Notes for more information.

•

Click the arrow to reopen the completed report dialog used to generate this output.

•

Click the gray border to the left of the Options tab to open a dynamic report navigator that lists all of the reports in the review. Refer to Report Navigator for more information.

Methodology

This report compares the summary statistic of each site compared to all other sites taken together as a reference.

•

Mean - An unpaired t-test assuming unequal variances between the groups is used.

FDR p-values are calculated and the reference line is determined as described in How does JMP Clinical calculate the False Discovery Rate (FDR)?.

•

Variance - A test of unequal variance is

used. FDR p-values are calculated and the reference line is determined as described in How does JMP Clinical calculate the False Discovery Rate (FDR)?.

•

Skewness and Kurtosis - No statistical tests are performed.

Report Options

Findings Analysis

By default the report is set to analyze all tests from all findings domains. You can opt however, to restrict the search to specific Findings Tests.

You can specify whether to search all results in original units when you Analyze: the data or restrict the search to either character results (in standard format) or numeric results (in standard units).

You can opt to Consider BY variables in the analysis. This option, which assumes that BY variables (left vs. right arm for collecting blood pressure data, for example) are included in the experimental design, is selected by default. You can uncheck this option to ignore BY variables.

Use the Only include BY variables if they are domain keys option to subset the available variables to only include those variables that are domain keys. If the option is unchecked, the report uses the cross-classification of xxCAT, xxSCAT, xxLOC, xxMETHOD, xxPOS, xxSPEC, and xxTPT for creating by groups for all variables that are available (as it had in the past).

The Summarize sites with at least this many subjects: option enables you to set a minimal threshold for the sites to be analyzed. Only those sites which exceed the specified number of subjects are included. This feature is useful because it enables you to exclude smaller sites, where small differences due to random events are more likely to appear more significant than they truly are. In larger sites, observed differences from expected attendance due to random events are more likely to be significant because any deviations due to random events are less likely to be observed.

By default, this report summarizes the means across the study. Optionally, you can choose to Analyze for: variance, skewness, or kurtosis.

Check the Generate summary statistics by visit to summarize the data for each visit in addition to the overall summary.

Unscheduled visits can occur for a variety of reasons. By default, these are excluded from this analysis. However, by unchecking the Remove unscheduled visits box, you have the option of including them.

The Alpha option is used to specify the significance level by which to judge the validity of the summary statistics generated by this report. By definition, alpha represents the probability that you will reject the null hypothesis when the null is, in fact, true. Alpha can be set to any number between 0 and 1, but is most typically set at 0.01, 0.05, or 0.10. The higher the alpha, the lower your confidence that the results you observe are correct.

Filtering the Data:

Filters enable you to restrict the analysis to a specific subset of subjects and/or adverse events, based on values within variables. You can also filter based on population flags (Safety is selected by default) within the study data.

See Select the analysis population, Select saved subject filter 1, and Additional Filter to Include Subjects

The Subset of Visits to Analyze options enables you to restrict to a specific subset of visits.