Hi all,
I have a question about gene ontology/GSEA and reactome analyses on scRNAseq dataset. I don't understand on which genes/clusters is correct to perform these analyses? Do I have to perform these analysis on all clusters (post filtering, normalization and scaling) or they should be performed on subclusters (eg. only immune cells).
If the 2nd case if the correct approach, but I have an integrated dataset (treated vs control) do I have to consider only one condition (eg. immune cell- treatement) or both?
Eg. GSEA analyses needs to be performed on the whole dataset if you have bulk-RNAseq dataset so I wonder if the same principle apply also to scRNAseq and how to consider anf integrated dataset.
I hope it make sense my question.
Thank you!
Camilla
