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FindMarkers from Seurat returns p values as 0 for highly significant genes
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Norman Nicolson
FindMarkers from Seurat returns p values as 0 for highly significant genes
I prefer to apply a threshold when showing Volcano plots, displaying any points with extreme / impossible p-values (e.g. < 10e-20) with a different symbol at the top of the graph.
However, a better approach is to avoid using p-values as quantitative / rankable results in plots; they're not meant to be used in that way. You can show results as a MA plot instead, plotting log2 fold change vs average expression:
It's a bit trickier to get expression values out of Seurat because they're not currently calculated in the FindMarkers results tables, so you'll need to manually subset the cells and calculate mean expression on a per-marker basis.
I prefer to apply a threshold when showing Volcano plots, displaying any points with extreme / impossible p-values (e.g. < 10e-20) with a different symbol at the top of the graph.
However, a better approach is to avoid using p-values as quantitative / rankable results in plots; they're not meant to be used in that way. You can show results as a MA plot instead, plotting log2 fold change vs average expression:
It's a bit trickier to get expression values out of Seurat because they're not currently calculated in the FindMarkers results tables, so you'll need to manually subset the cells and calculate mean expression on a per-marker basis.
It was really helpful solution. I used the AverageExpression(object = pbmc_small) to get mean expression per cell type. then combed it with the Find Markers results using the Gene names then was able to perform MA plot. So those genes are visible under the plot now. - Thanks a lotMore
I prefer to apply a threshold when showing Volcano plots, displaying any points with extreme / impossible p-values (e.g. < 10e-20) with a different symbol at the top of the graph.
However, a better approach is to avoid using p-values as quantitative / rankable results in plots; they're not meant to be used in that way. You can show results as a MA plot instead, plotting log2 fold change vs average expression:
It's a bit trickier to get expression values out of Seurat because they're not currently calculated in the FindMarkers results tables, so you'll need to manually subset the cells and calculate mean expression on a per-marker basis.
I prefer to apply a threshold when showing Volcano plots, displaying any points with extreme / impossible p-values (e.g. < 10e-20) with a different symbol at the top of the graph.
However, a better approach is to avoid using p-values as quantitative / rankable results in plots; they're not meant to be used in that way. You can show results as a MA plot instead, plotting log2 fold change vs average expression:
It's a bit trickier to get expression values out of Seurat because they're not currently calculated in the FindMarkers results tables, so you'll need to manually subset the cells and calculate mean expression on a per-marker basis.
More
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