Help on options
- This icon indicates a rough estimate of the time that will be needed to perform all the panel computations (including cross-validation and pre-filtering if those are selected). This time is subject to many variations (such as server load, or some characteristics of the data) but should give a good idea of the order of magnitude of computation time (second, minutes, hours, days or years).
- Maximum panel size
- This number is the maximum size you want your panels to be. For instance, to test for panels containing 1, 2, 3 or 4 biomarkers, set this list to 4.
- Specificity or sensitivity : the focus of your panel: do you want to have a high specificity or sensitivity ?
- Number: this number defines the minimum specificity or sensitivity (depending on your choice above) that must be achieved by a panel to be retained. All panels that doesn't reach this performance will be discarded.
0.95(the default), PanelomiX will optimize the sensitivity of panels with at least 95% of specificity.
Cross-validation (CV) is used to assess the stability of panels. Choose
yes to enable cross-validation (enabled by default).
More details about cross-validation on wikipedia.
- Cross-validation folds
- Determines in how many parts the data will be divided for CV.
- Cross-validation repeats
- Cross-validation can be repeated to get better estimates of the stability, but more repeats mean longer computation time.
Pre-filtering is sometimes required to speed-up the computation. Choose
yes to enable pre-filtering (disabled by default).
- Number of markers
- Only this number of markers will be used in the computations. If more markers are selected in the details, only those being selected as split points most often will be retained.
- Number of thresholds
- Several thresholds are tested for each markers. By default, these thresholds are the ROC curve local maximas. If an integer N is defined here, only the N thresholds being selected most often as split points for the given marker will be retained.
The output options define how the results will be presented.
- Desired output format
- With âHTML onlyâ, a simple HTML output is produced. This is the fastest option, best used during early screening steps.
- If âPDF reportâ is selected, a PDF file is generated summarizing the results (including cross-validation if this option was selected above). A ROC analysis is performed without computing confidence intervals.
- When âPDF report with confidence intervalsâ is checked, the PDF report is generated as above, but ROC curves come with additional confidence intervals for (p)AUC, sensitivity and specificity. This is most complete but also the slowest option.
- Skip cross-validation of individual biomarker
- Check this box only if running the panel with cross-validation results in an error message saying âCannot cross-validate the best biomarker. Most likely, its performance is too low. Try again and if the problem persists, disable cross-validation.â This message means that the best biomarker could not meet the performance requirements defined above in the âMinimum Accuracy/Sensitivity/Specificity Numberâ. In this case, no panel is found and the cross-validation cannot succeed, causing the PDF export to abort. With this option checked, this part of the cross-validation will be ignored and the PDF export will succeed.