IDR Consistency
Check replicate consistency from IDR values.
Description
IDR consistency summarizes values already estimated by a statistical pipeline.
IDR consistency summarizes values already estimated by a statistical pipeline.1
Check replicate consistency from IDR values.
When to use IDR Consistency
Use this tool to check replicate consistency from IDR values.
Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
How to use IDR Consistency and understand its results
- Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
- Enter idrValues, maximumIdr, minimumPassingPercent using the field table and calculation rules, then run the tool.
- Read passingCount, passingPercent, consistent. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| idrValues | Irreproducible discovery rates | list of number | Required |
| maximumIdr | Maximum passing IDR | number; minimum: 0; maximum: 1 | Required |
| minimumPassingPercent | Minimum passing share | number; minimum: 0; maximum: 100 | Required |
Enter nonempty IDR values and cutoff 0–1 and a required passing percentage 0–100. Return passing count, percentage and inclusive consistency flag.
passingPercent=100count(IDR≤maximumIdr)/n; consistent=passingPercent≥minimumPassingPercent Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| passingCount | Passing discoveries | integer; minimum: 0 |
| passingPercent | Passing discovery share | number; minimum: 0; maximum: 100 |
| consistent | Meets supplied consistency threshold | boolean |
{
"input": {
"idrValues": [
0.01,
0.02,
0.2,
0.03
],
"maximumIdr": 0.05,
"minimumPassingPercent": 70
},
"output": {
"passingCount": 3,
"passingPercent": 75,
"consistent": true
}
}Limitations and assumptions
No peak matching, ranking or IDR model is fitted.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Replicate Concordance: Calculate biological-replicate Pearson concordance and gate status. For a complementary task, use Probe Pvalue Filter: Exclude methylation probes failing a detection p-value threshold.
References
-
IDR Consistency — tool.io
Similar or alternative tools
- Replicate Concordance
Calculate biological-replicate Pearson concordance and gate status.
- Probe Pvalue Filter
Exclude methylation probes failing a detection p-value threshold.