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Interpretation of CytoSig results based on scRNA-seq data #3

Closed niehu2018 closed 2 years ago

niehu2018 commented 2 years ago

Hi, I used scRNA-seq data to compute the cytokine signaling activity with CytoSig. I got the z-score and p-value matrix (row by cell, col by cytokine). Q1: Does the z-score value reflect the signaling activity of cytokines? Q2: If I want to compare the cytokine activity between two cell types, should I only keep the cells with p-value < 0.05 or 0.01?

Best, Hu

data2intelligence commented 2 years ago

Q1: Yes. Q2: Please use Benjamini-Hochberg correction first to convert p-value to q-values (FDR). Then use FDR < 0.05.

niehu2018 commented 2 years ago

Thanks a lot. This solved my question!