I am working with single cell data and using seurat to analyze the results. Often in manuscript, we see the dotplots showing the expression of the marker genes or genes of interest across the different clusters. My question here is: a. When comparing expression of a gene (lets say geneA) across cluster, for example, lets say for cluster 0, the average expression for geneA that is plotted, is it calculated considering all the cells in the sample or all the cells in the cluster0? If it is calculating the average expresison based on total number cells present in cluster 0 (here), is it correct to compare the expression of geneA across all the clusters? Because among the different clusters, the number of cells are different, and the number of cells that are expressing geneA can vary alot across the clusters.

Thank you in advance!

  • 1
    $\begingroup$ Hi, could you please add more context to your question? An example image of a Seurat dotplot that demonstrates your issues would help a lot here. $\endgroup$
    – gringer
    Aug 11 at 1:27
  • $\begingroup$ Since it is showing mean expression among cells within a cluster, why would different number of cells across clusters worry you? $\endgroup$
    – Phoenix Mu
    Aug 11 at 16:36

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