Hi there,
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.
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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.
@munta @PierreBoyeau
I don’t think this is correct. With GSEA, you need to be able to asses if a pathway is enriched positively or negatively between treatment and controls. So you do need to rank the genes in a way that makes sense with direction of regulation. @munta For volcano plots the scVI tutorial uses ‘proba_not_de’ as equivalent to p-value to compute a -log10(proba_not_de) score, it has made sense in my analyses to rank with sign(lfc_median)*(-log10(proba_not_de))
Thanks @aj95b for that and you are right I did the same by taking (proba_not_de) as I wasn’t convinced to take bayes factor (@adamgayoso no offence).