discover_reference_stability
Ask whether the genes used to normalise expression (reference or housekeeping genes, such as GAPDH, ACTB or B2M) are more or less variable across human tissues than genes of the same abundance, on GTEx v8 median expression. Each candidate's standard deviation of log2(TPM + pseudocount) across the chosen tissues is ranked among the genes nearest it in mean expression (1,000 by default, from the 19,107 protein-coding genes GTEx measures), giving one p for 'more variable than its peers' and one for 'steadier', each corrected across the candidates. The four rankers the field runs (geNorm M, NormFinder, BestKeeper, comparative ΔCt, and RefFinder's consensus) also order the candidates against each other, reading the tissues as samples. A ranker always finds a most stable gene; the null says whether any candidate is stable at all. Tissue medians hide the variation between people within a tissue, so this answers 'across tissues', not 'across samples of one tissue'.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| alpha | No | false discovery rate at which a candidate is called more variable, or steadier, than its peers. | |
| genes | Yes | the candidate reference genes, as current HGNC symbols (GAPD is GAPDH). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| tissues | No | GTEx tissue names to compare across, three or more; empty means all 54. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| correction | No | Benjamini–Hochberg (independent or positively dependent tests) or Benjamini–Yekutieli (any dependence; less power). Values: BH (Benjamini–Hochberg), BY (Benjamini–Yekutieli). | BH |
| neighbours | No | how many genes nearest in mean expression each candidate is ranked among. The smallest p it can give is 1 / (neighbours + 1). | |
| pseudocount | No | added to TPM before the logarithm, so a tissue with no expression has one. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes | the full result | |
| stable | Yes | the candidates steadier than their expression peers at the chosen false discovery rate | |
| rankers | Yes | geNorm M, NormFinder, BestKeeper, comparative ΔCt and the RefFinder consensus over the candidates | |
| unstable | Yes | the candidates more variable across tissues than their expression peers at the chosen false discovery rate | |
| candidates | Yes | every candidate's mean and SD of log2 expression, the expression band of its peers, its percentile among them and both p and q |