Bestkeeper Stability

Screen reference-gene Ct stability by replicate standard deviation.

Description

Reference-gene Ct spread can be screened before normalization.

Reference-gene Ct spread can be screened before normalization. Here SD is computed over each supplied replicate row with the population denominator.^[1]

Screen reference-gene Ct stability by replicate standard deviation.

When to use Bestkeeper Stability

Use this tool to screen reference-gene Ct stability by replicate standard deviation.

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 Bestkeeper Stability 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 referenceGeneIds, ctReplicates, maximumStdDev using the field table and calculation rules, then run the tool.
Read stableGeneIds, standardDeviations. 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
referenceGeneIds	Reference gene ids	list of string	Required
ctReplicates	Ct replicates	list of list of number	Required
maximumStdDev	Maximum std dev	number	Required

Enter nonempty reference IDs with one row of at least two finite Ct values per gene and a finite maximum SD. Return population SD values in gene order and passing IDs. Rows may have different replicate counts.

SD_g=sqrt(Σ(Ct−meanCt)²/n); stable if SD≤maximum

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

Output field	Meaning	Value type
stableGeneIds	Stable gene ids	list of string
standardDeviations	Standard deviations	list of number

json

{
  "input": {
    "referenceGeneIds": [
      "a",
      "b"
    ],
    "ctReplicates": [
      [
        20,
        20,
        20
      ],
      [
        20,
        22,
        24
      ]
    ],
    "maximumStdDev": 1
  },
  "output": {
    "stableGeneIds": [
      "a"
    ],
    "standardDeviations": [
      0,
      1.632993161855452
    ]
  }
}

Limitations and assumptions

This is an SD screen rather than full BestKeeper correlation/index analysis. No Ct sentinel processing, sample-quality handling or reference normalization is included.

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

Bestkeeper Stability — 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.