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OWClusterAnalysis: Cluster-vs.-cluster instead of one-vs.-all

Open mstrazar opened this issue 7 years ago • 2 comments

Perhaps applies to differential gene expression in general; If we want to find cluster specific genes, we have to compare the expression in cluster A to its most similar cluster. Otherwise, the rest of the clusters will occlude the results and we will get the genes that do not really differentiate cluster A from all of the other clusters.

mstrazar avatar Jun 04 '18 14:06 mstrazar

One possible solution is to compute a per-cluster p-value and use the maximum across clusters.

mstrazar avatar Jun 04 '18 14:06 mstrazar

I see two use cases:

  • I would like to identify genes that differentiate a cluster from all others (marker genes). As an example, I want to label a cluster as a cell type based on the marker genes.

  • I want to know differentially expressed genes between two considers in a given cluster. As an example, I want to know differentially expressed genes in before and after treatment in B-cells.

anupparikh avatar Jun 04 '18 21:06 anupparikh