Seurat -Compare clusters

Description

Find the markers for a specific cluster compared to another cluster(s).

Parameters

Details

Seurat function FindMarkers is used to identify positive and negative marker genes for the clusters of interest, determined by the user. By default, differentially expressed genes are tested between the cluster of interest and all the other cells by default. User can also define to compare the cluster of interest to another cluster or clusters by typing the numbers of the clusters to compare to in the parameter field. When comparing to group of clusters, separate the clusters with a comma (,).

You can filter out genes prior to statistical testing by requiring that a gene has to be expressed in at least a certain fraction of cells in either of the two groups (min.pct=0.25). You can also require that the change in expression has to be at least certain percentage between the groups (thresh.test=0.25). Both of these parameters can be set to 0, but with a dramatic increase in time since this will test a large number of genes that are unlikely to be highly discriminatory.

The marker genes for each cluster are written in the markers.tsv file.

Seurat currently implements the following tests:

The "Poisson" and "negbiom" options should ONLY be used on UMI datasets, as they assume an underlying poisson and negative-binomial distribution, respectively. Please note that the DESeq2 method has not been included, because it was not designed for situations where there are thousands of samples (cells) and it is therefore very slow.

The markers.tsv result file contains marker genes and associated statistics for all the clusters:

For more details, please check:
The Seurat tutorials

Output