Thanks for the tool. I have used scvi differential expression to get DE genes. Now, I want to proceed to do GSEA analysis (with another tool) so I have to rank the genes for that. Generally, I use sign(lfc)*pvalue for ordering genes. But, in scvi de results there is no p-value (I got delta=0.25 for all genes). Also, not sure which should I use lfc_mean or lfc_median? So, do you have any idea that you can help me with regarding this. Many thanks.
You can use the Bayes factor, where higher would indicate more likelihood of the hypothesis that there is differential expression (note that this is not interpreted exactly the same as a p-value).
I would start with LFC median as it’s more likely to get the sign correct, where mean can be influenced by outliers.