I'm running FindAllMarkers

markers <- FindAllMarkers(scData_scTransform_PTX_only_res04_20PC_6000g_30mt_sb_removal_20210713_ann_exp0_counts, min.pct = 0.25, logfc.threshold = 0.25)

But was wondering if there is a function in seurat to get the raw (non-normalized) expression data from each cell type cluster

  • $\begingroup$ Hi, could you please add more context to this question so that we can understand why you want to find out this information? I've calculated cell counts per cluster, and visualised gene counts per cluster using scatter plots, but haven't yet run into a case where I'd need to work out gene count per cluster as a single statistic (whatever that means). $\endgroup$
    – gringer
    Aug 11 '21 at 12:51
  • $\begingroup$ @mmpp could it be that you meant to compare expression profiles of some genes (by means of a boxplot, for instance), to evaluate the differences between two conditions, in the same cell type, i.e. a cluster? $\endgroup$
    – gabt
    Aug 20 '21 at 8:45
  • $\begingroup$ are you trying to calculate pseudobulk average? $\endgroup$
    – Dr_Hope
    Sep 15 '21 at 21:58

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