The first step in any new analysis is to perform normalization. The normalization command performs different actions, depending on the workflow. A Standard Compute runtime is required.
To run normalization, click the Normalize button in the top bar of workbench.
Single cell RNA-seq:
1
Normalize total
Normalizes each cell by total counts over all genes, so that every cell has the same total count after normalization (target = 10,000).
2
Log transform
Takes log1p of normalized counts.
3
Compute highly variable genes
Uses the seurat flavor of the algorithm with a gene threshold of 2,000.
4
Scale counts
Uses a max value of 10.
Bulk RNA-seq
1
Normalize counts
Uses TMM (Trimmed Mean of M component) to make samples comparable.
2
Log transform
Takes log1p of normalized counts.
3
Scale counts
Uses a max value of 10.
For each dataset, Panomics keeps a copy of the raw counts and a copy of the unscaled normalized and log-transformed counts alongside the scaled version.
