calculate_rnaseq_power
Read-only
Sample size and power for an RNA-seq comparison of two groups, one gene at a time: the biological replicates per group needed to detect a fold change at a given sequencing depth and within-group coefficient of variation, or the power, detectable fold change, CV or α a fixed design gives. Leave one of n, cv, effect, alpha and power out (or name it in solve_for). Every quantity takes a list, and the answer is the whole grid, so depth against replicates is one call. RNASeqPower 1.52.0 (Hart et al. 2013), reproduced: a negative binomial count with Poisson sequencing noise 1/depth plus biological variance CV².
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| n | No | biological replicates in group 1 (and in group 2, unless `n2` is given). | |
| cv | No | the biological coefficient of variation within a group: 0.4 or less for most genes in human studies, about 0.1 in inbred animals (Hart et al.). | |
| n2 | No | replicates in group 2, one per `n`. Advanced. | |
| cv2 | No | the CV within group 2, one per `cv`. Advanced. | |
| alpha | No | α, the two-sided false-positive rate per gene. | |
| depth | Yes | average depth of coverage of the gene: its expected read count per sample. Hart et al. found most genes at 0.1 per million mapped reads, so 4 at 40 million. | |
| power | No | 1 − β, the chance of detecting the change if it is real. No default: the target is yours to choose. | |
| _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. | |
| effect | No | the fold change to detect; 2 and 0.5 are the same change. | |
| _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. | |
| solve_for | No | the quantity to solve. Left unset, it is the one of n, cv, effect, alpha and power that was not given. Values: n (n per group), cv (CV), effect (fold change), alpha (α), power (power). |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| grid | Yes | every design in the grid: each quantity, and the solved one | |
| curve | Yes | the solved quantity along the first quantity given as a list, one line per value of the second | |
| rCall | Yes | the R call that reproduces the grid | |
| value | Yes | the solved value, when the design is a single cell | |
| solved | Yes | which quantity was solved |