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reactome / ReactomeGSA-tutorials

Tutorials on how to use the ReactomeGSA R package.
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HEATMAP group-wise e.g, Control, Patient_Early, Patient_Late #2

Open Deepesh123gupta opened 2 years ago

Deepesh123gupta commented 2 years ago

This is great platform to look for pathway significance. Currently, I am analyzing scRNAseq data where I have three groups (9 samples or triplicates). I would like to know gene set pathway analysis between three groups .

  1. Do you think that this ReactomeGSA( ssGESA) HEATMAP would be helpful in my case e.g. X-axis: Three Groups Y-axis: Pathways?
  2. Would it be possible to have HEATMAP with X-axis: each clusters with three groups Y-axis: Pathways?

Thanks!

jgriss commented 2 years ago

Hi @Deepesh123gupta,

Thanks a lot for your interest in ReactomeGSA!

The heatmap function is really only a visualization tool. Since you actually have a group-wise comparison, you could first use the ssGSEA function to get the expression values per cluster / cell type and sample. And then in a second step use f.e. limma to calculate a differential expression between your groups on the pathway level.

Kind regards, Johannes