3 posts
A step-by-step guide to taking a protein abundance matrix, building a defensible ranking statistic, and running over-representation and rank-based enrichment in R, including how to read a negative enrichment score.
A working guide to running KEGG enrichment on personal RNA-seq: quantification, identifier mapping, GSEA versus over-representation, reading the maps, and the failure modes that make most pathway results meaningless.
A practical guide to Gene Ontology analysis of RNA-seq: building a defensible gene list, correcting for length and expression bias, running overrepresentation tests and GSEA in R, and collapsing redundant terms into something you can read.