Genorm M Value

Rate candidate reference genes by mean pairwise log-expression variation.

Description

Pairwise log-expression variation compares candidate reference genes across aligned samples.

Pairwise log-expression variation compares candidate reference genes across aligned samples. Stable ratios can be useful even when individual expression levels differ.^[1]

Rate candidate reference genes by mean pairwise log-expression variation.

When to use Genorm M Value

Use this tool to rate candidate reference genes by mean pairwise log-expression 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 Genorm M Value 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, logExpressions using the field table and calculation rules, then run the tool.
Read mValues, mostStableGeneId. 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
logExpressions	Log expressions	list of list of number	Required

Enter at least three IDs and matching gene rows with at least two common sample columns. Calculate each pair's differences, their population SD using the sample-count denominator and each gene's mean pairwise SD. Return M values and the first gene attaining minimum M.

M_i=mean over j≠i of populationSD(logExpression_i−logExpression_j)

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

Output field	Meaning	Value type
mValues	M values	list of number
mostStableGeneId	Most stable gene id	string

json

{
  "input": {
    "geneIds": [
      "a",
      "b",
      "c"
    ],
    "logExpressions": [
      [
        1,
        2,
        3
      ],
      [
        1,
        2,
        4
      ],
      [
        1,
        2,
        5
      ]
    ]
  },
  "output": {
    "mValues": [
      0.7071067811865475,
      0.4714045207910317,
      0.7071067811865475
    ],
    "mostStableGeneId": "b"
  }
}

Limitations and assumptions

Log values must already use a consistent base and transformation. This is one pass over candidates, without iterative geNorm elimination, normalization-factor variation or group modeling.

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 Normfinder Group Variance: Estimate reference-gene between-group variance for stability screening.

References

Genorm M Value — tool.io

Similar or alternative tools

Housekeeping Cv Rank
Rank housekeeping genes by replicate coefficient of variation.
Normfinder Group Variance
Estimate reference-gene between-group variance for stability screening.