Pseudocount Plus-One Zero-Avoidance Applier

Apply an explicit plus-one pseudocount to nonnegative integer expression counts; not a fitted normalization model.

Description

Apply an explicit plus-one pseudocount to nonnegative integer expression counts; not a fitted normalization model.

Adding one to count data is a simple pseudocount transform that avoids zeros for some later operations. Its consequences depend on the downstream statistical method.

When to use this tool

Apply an explicit plus-one pseudocount to nonnegative integer expression counts; not a fitted normalization model.

  • Prepare the supplied counts 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

  1. Enter counts. Use the exact text syntax, units and index conventions explained below.
  2. Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
  3. Read result.plusOneCounts. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.

Require every count to be an integer from zero through one trillion, then return count+1 for each entry in the original order.1

Input fieldMeaning and representationAccepted input
countscounts.List of finite numbers; bounded by the operation
Output fieldInterpretation
resultObject containing the named outputs below.
result.plusOneCountsThe plus one counts list in the ordering and representation described above.
json
{
  "input": {
    "counts": [
      0,
      2
    ]
  },
  "output": {
    "result": {
      "plusOneCounts": [
        1,
        3
      ]
    }
  }
}

Limitations and assumptions

  • This is not normalization or a recommended pseudocount for every analysis. No logarithm, library-size adjustment or model fit is applied, and low counts can change proportionally more than high counts.
  • 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

  1. Tool behavior and example: Pseudocount Plus-One Zero-Avoidance Applier — tool.io

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