Housekeeping Cv Rank

Rank housekeeping genes by replicate coefficient of variation.

Description

A reference gene's coefficient of variation compares replicate spread with its mean.

A reference gene's coefficient of variation compares replicate spread with its mean. This implementation uses population SD, so its denominator is the number of supplied replicates.^[1]

Rank housekeeping genes by replicate coefficient of variation.

When to use Housekeeping Cv Rank

Use this tool to rank housekeeping genes by replicate coefficient of variation.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Housekeeping Cv Rank and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter geneIds, expressionReplicates using the field table and calculation rules, then run the tool.
Read cvPercents, rankedGeneIds. 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
geneIds	Gene ids	list of string	Required
expressionReplicates	Expression replicates	list of list of number	Required

Enter nonempty IDs with one row of at least two finite replicates each. Require each row's mean to be positive, compute population CV and return values in original gene order plus IDs ranked ascending. Ties retain input order; rows may differ in length.

CV%=100 sqrt(Σ(x−mean)²/n)/mean; rank lowest CV first

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
cvPercents	Cv percents	list of number
rankedGeneIds	Ranked gene ids	list of string

json

{
  "input": {
    "geneIds": [
      "a",
      "b"
    ],
    "expressionReplicates": [
      [
        10,
        10
      ],
      [
        10,
        20
      ]
    ]
  },
  "output": {
    "cvPercents": [
      0,
      33.33333333333333
    ],
    "rankedGeneIds": [
      "a",
      "b"
    ]
  }
}

Limitations and assumptions

Individual signed values are accepted if the mean is positive. This is not a full reference-gene stability model and does not account for group structure or measurement uncertainty.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Matrices are limited to 128 rows and 128 entries per row; other lists are limited to 100,000 entries. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Normfinder Group Variance: Estimate reference-gene between-group variance for stability screening. For a complementary task, use Bestkeeper Stability: Screen reference-gene Ct stability by replicate standard deviation.

References

Housekeeping Cv Rank — tool.io

Similar or alternative tools

Normfinder Group Variance
Estimate reference-gene between-group variance for stability screening.
Bestkeeper Stability
Screen reference-gene Ct stability by replicate standard deviation.