Normfinder Group Variance

Estimate reference-gene between-group variance for stability screening.

Description

Between-group reference-gene variation can be screened using group means.

Between-group reference-gene variation can be screened using group means. Those means do not provide the within-group information needed for a full NormFinder stability model.^[1]

Estimate reference-gene between-group variance for stability screening.

When to use Normfinder Group Variance

Use this tool to estimate reference-gene between-group variance for stability screening.

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 Normfinder Group Variance 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, groupMeans, maximumBetweenGroupVariance using the field table and calculation rules, then run the tool.
Read betweenGroupVariances, stableGeneIds. 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
groupMeans	Group means	list of list of number	Required
maximumBetweenGroupVariance	Maximum between group variance	number	Required

Enter nonempty gene IDs and one row of at least two finite group means for each gene. Calculate population variance of each row and retain IDs with variance at most the supplied finite maximum. Rows may contain different group counts.

betweenVariance=Σ(groupMean−meanOfGroupMeans)²/numberOfGroups

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

Output field	Meaning	Value type
betweenGroupVariances	Between group variances	list of number
stableGeneIds	Stable gene ids	list of string

json

{
  "input": {
    "geneIds": [
      "a",
      "b"
    ],
    "groupMeans": [
      [
        10,
        11
      ],
      [
        10,
        14
      ]
    ],
    "maximumBetweenGroupVariance": 1
  },
  "output": {
    "betweenGroupVariances": [
      0.25,
      4
    ],
    "stableGeneIds": [
      "a"
    ]
  }
}

Limitations and assumptions

This is a between-group variance screen, not full NormFinder: group sample sizes and within-group variation are omitted. A negative criterion simply retains no genes.

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 Housekeeping Cv Rank: Rank housekeeping genes by replicate coefficient of variation. For a complementary task, use Genorm M Value: Rate candidate reference genes by mean pairwise log-expression variation.

References

Normfinder Group Variance — tool.io

Similar or alternative tools

Housekeeping Cv Rank
Rank housekeeping genes by replicate coefficient of variation.
Genorm M Value
Rate candidate reference genes by mean pairwise log-expression variation.