Crate rsomics_limma_ebayes 

lmFit + eBayes + topTable(sort.by=“none”) for a log-expression matrix.

Clean-room reimplementation of limma’s moderated t-statistic pipeline: Smyth (2004), Stat Appl Genet Mol Biol 3(1):3, doi:10.2202/1544-6115.1027. No limma (GPL) source was consulted; the method follows the published paper and is validated black-box against the binary.

Structs

Options

Results

Row

topTable(sort.by=“none”) row, in input gene order.

Functions

read_contrast

Contrast TSV: first column = original coefficient name, header = contrast names. Entry [coef][contrast] is the contrast weight.

read_design

Design TSV: first column = sample id, header first cell may be empty or a label; remaining columns are coefficient names with numeric model-matrix entries (one row per sample, in sample order).

read_expr

run

write_results