1 Pseudobulk

A pseudobulk sample is formed by aggregating the expression values from a group of cells from the same individual. The cells are typically grouped by clustering or cell type assignment. Individual refers to the experimental unit of replication (e.g., the individual mice or patients).

Forming pseudobulk samples is important to perform accurate differential expression analysis. Cells from the same individual are more similar to each other than to cells from another individual. This means treating each cell as an independent sample leads to underestimation of the variance and misleadingly small p-values. Working on the level of pseudobulks ensures reliable statistical tests because the samples correspond to the units of replication.

We can use pseudobulks for example to find the expression changes between two conditions for one cell type.

2 Example