UMAP

The UMAP command in Panomics performs multiple processing steps. A Standard Compute runtime is required.

1

Runs batch effect correction algorithm (optional)

Algorithm	Microarray	Bulk RNA-seq w/ normalized counts	Bulk RNA-seq w/ raw counts	Single Cell RNA-seq
Limma	✅	✅	❌	❌
Combat	✅	✅	❌	❌
CombatSeq	❌	❌	✅
Harmony *	❌	❌	❌	✅
scVI	❌	❌	❌	✅

2

Runs PCA

3

Computes neighborhood graph

Uses 15 neighbors and the PCA representation based on batch effect correction algorithm choice.

4

Computes UMAP

* The Harmony batch effect correction algorithm operates on the PCA space, so PCA is computed first and then replaced by the harmonized PCA.

In the following example, we perform normalization, then UMAP with no batch correction. Coloring the embedding by the diagnosis and sample name observations reveals strong batch effects. We then run UMAP again with Harmony batch effect correction.

Normalize & UMAP