Downregulated Gene Count Tally at FDR Gate Counter
Count direction-specific genes at a supplied adjusted-p gate; zero effect is neither up nor down. Does not calculate FDR or establish biological relevance.
Description
Count direction-specific genes at a supplied adjusted-p gate; zero effect is neither up nor down.
A directional differential-expression gate combines the sign of a fold change with an already adjusted significance value. Keeping the adjustment external makes the selection rule explicit.
When to use this tool
Count direction-specific genes at a supplied adjusted-p gate; zero effect is neither up nor down.
- Prepare the supplied log2FoldChanges, adjustedPValues, maximumFdr fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter log2FoldChanges, adjustedPValues, maximumFdr. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.selectedCount, result.selectedIndexes. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require nonempty aligned log2FoldChanges/adjustedPValues and all adjusted values plus maximumFdr within zero through one. Select indexes with strictly negative log2 fold change and adjusted p value at most maximumFdr; return their count and indexes.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| log2FoldChanges | log2 fold changes. | List of finite numbers; bounded by the operation |
| adjustedPValues | adjusted pvalues. | List of finite numbers; bounded by the operation |
| maximumFdr | maximum fdr. | Finite number; from zero through one inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.selectedCount | The selected count value under the stated formula or text convention. |
| result.selectedIndexes | The selected indexes list in the ordering and representation described above. |
{
"input": {
"log2FoldChanges": [
-1,
0,
1
],
"adjustedPValues": [
0.01,
0.01,
0.01
],
"maximumFdr": 0.05
},
"output": {
"result": {
"selectedCount": 1,
"selectedIndexes": [
0
]
}
}
}Limitations and assumptions
- The tool does not adjust p values, fit an expression model or require a minimum fold-change magnitude. Zero fold changes are excluded; the gate does not independently prove biological downregulation.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Use a complete assay-analysis workflow for normalization, quality control and inference. Keep supplied measurements, fixed educational windows and caller-chosen thresholds distinct; these tools perform the documented calculation or retrieve a short reference note.
References
Similar or alternative tools
- Upregulated Gene Count Tally at FDR Gate Counter
Count direction-specific genes at a supplied adjusted-p gate; zero effect is neither up nor down.
- lncrna coding potential gate
A supplied coding-potential score can be compared with a noncoding cutoff.