Open domi84 opened 1 year ago
Those are not reported as they do not exist. This method only maps pathway expression values onto the clusters (ie. one pathway expression level per cluster). In order to get p- / FDR values you would perform a f.e. t-test on these values comparing the relevant groups of clusters with each other.
Does that make sense?
Yes, it makes sense,
In order to get p- / FDR values you would perform a f.e. t-test on these values comparing the relevant groups of clusters with each other.
I assume you don't have a function ready to use in the package, because I don't see it in the vignette https://bioconductor.org/packages/release/bioc/vignettes/ReactomeGSA/inst/doc/analysing-scRNAseq.html
Also, because those are pathway-level expression values per cell cluster, do I need to split them per replicates (donors) in order to make a stat test?
Hi,
We are working on a function - but as always, things don't progress as quickly as we'd like.
Yes, splitting based on donor is ideal for this setup.
Hello, thanks for this package, seems pretty useful. I am trying to use it on a scRNAseq dataset (Seurat), I get the results, I can see pathways, but I don't see any FDR/p-value columns. I checked also the PDF/excel files generated, but nothing. How can I access to those?