Finding DEG between 2 clusters

My dataset has 4 samples. After data integration and clustering, I want to obtain DEG between any 2 clusters. How can I do that? Under “Batch differential expression table” option 1, I can compare any cluster to the rest. Option 3 seems to compare any 2 clusters, but it outputs 4 files. Why 4? Is it comparing something like cluster 1 in sample A vs. cluster 2 in sample A instead of cluster 1 in all samples vs. cluster 2 in all samples? I am confused.


Thanks for the post!

I’m not sure I fully understand what you mean by “I want to obtain DEG between any 2 clusters” - do you mean within a specific sample or across all samples or something else?

In the Differential Expression tool in the Data Exploration module, you can select the comparison you’d like to perform. For example, using the first toggle option (‘within’) you can compare cluster 1 to cluster 2 OR cluster 1 to all other clusters. You can select to do this using cells from a specific sample or group (cluster 1 in sample A versus cluster 2 in sample A) or across all cells in the dataset (cluster 1 in all samples versus cluster 2 in all samples). Using the second toggle option (‘between’) you can compare a selected cluster between samples or groups, such as cluster 1 in sample A versus cluster 1 in sample B.

In the batch differential expression table, option 3 “Compare two cell sets for all samples/groups” allows you to compare cell sets (e.g. cluster 1 versus cluster 2 OR cluster 1 versus everything else) in bulk for all of your samples or groups. So if you have 6 samples in your dataset, you’ll get 6 output files - one for each sample.

Does this make sense? Can you tell me some more about your specific use case and whether or not I’ve covered it in my answer?