KEGG passway analysis after Seurat analysis
Hello, everyone. I am so sorry for this amateur question.
I have a scRNA-seq data and want to compare and visualize the expression levels across genes on a cluster by using clusterprofiler package (passway analysis), but I think the average expression levels of each gene can not be compared because these are not the same scale.
So I tried 3 steps as follows.
First, I selected a passway that I wanted to use.
Second, I calculated average expression of each cluster for each gene.
Third, I scaled them for each gene.
I think this is as same as Seurat DotPlot function, however, my method does not reflect the percentage of cells expressing the genes.
My question is
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Does this method valid? or has risks?
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Is logFC better than other transformations to try passway analysis when we use Seurat results?
Thank you.
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