Glossary

Glossary

Term	Definition
BH / FDR	Benjamini–Hochberg procedure; controls the expected proportion of false discoveries among significant results
CAMERA	Competitive gene-set test that adjusts for inter-gene correlation (limma)
Competitive test	Tests whether a set is more affected than other genes
CPM	Counts per million: counts divided by library size, times 10⁶
eBayes	Empirical-Bayes moderation of gene-wise variances toward a common prior (limma)
filterByExpr	edgeR's design-aware low-expression filter
FRY	Fast rotation gene-set test; self-contained (limma)
GSEA	Gene set enrichment analysis on a ranked gene list
Hidden module	A module significant as a whole while fewer than 25% of its members are individually significant
Homology family	A group of mouse and human genes connected through shared homology classes
Leading edge	The GSEA set members that drive the enrichment score
log₂FC	Log₂ fold change between two groups
MDS	Multidimensional scaling; limma's plotMDS uses leading log₂FC distances
Moderated F	Empirical-Bayes F test for any difference among groups
Moderated t	Empirical-Bayes t test (limma)
Module score	Per-sample mean z-score of a gene set's members
NES	Normalized enrichment score (GSEA)
ORA	Over-representation analysis; hypergeometric test of list overlap
RLE	Relative log expression: each gene's value minus its median across samples
RRHO	Rank–rank hypergeometric overlap
Self-contained test	Tests whether a set is differentially expressed at all
Silhouette	Measure of how well each item fits its cluster relative to the nearest other cluster (−1 to 1)
TMM	Trimmed mean of M-values normalization (edgeR)
voom	Precision weights from the mean–variance relationship of log-counts (limma)