Enrichr, Prerank, GSEA or ssGSEA?
Bioinformatician’s main tool for discovery has often been differential expression analysis. But between Enrich, Prerank, GSEA, ssGSEA, which tool should you use? here is the quick reminder X-plainer:
Enrichr is when you just have a list of genes (can be small):
GENEA, GENEB, GENEC
Prerank is when you have values that you can rank your list of genes from:
| Gene | Value |
|---|---|
| GENEA | 12 |
| GENEB | 8 |
| GENEC | 4 |
GSEA works best when you have a list of genes, with values associated with them across multiple conditions (and replicates):
| Gene | C1 | C2 | C3 | D1 | D2 | D3 |
|---|---|---|---|---|---|---|
| GENEA | 12 | 7 | 3 | 1 | 1 | 0 |
| GENEB | 8 | 0 | 6 | 8 | 1 | 1 |
| GENEC | 4 | 4 | 3 | 2 | 3 | 4 |
ssGSEA is when you have many values associated with them but not 2 specific condition and want to compare 1 vs the rest
| Gene | A | B | C | D | E | F |
|---|---|---|---|---|---|---|
| GENEA | 12 | 7 | 3 | 1 | 1 | 0 |
| GENEB | 8 | 0 | 6 | 8 | 1 | 1 |
| GENEC | 4 | 4 | 3 | 2 | 3 | 4 |
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