Hi all,
I was asked to perform exploratory analysis for scRNA-seq. I am new to this kind of analysis and I’m not sure how to decide on a couple of things. As I said in the title, I have only one sample per condition.
I did the PCA plot to see whether I should use merge or integrate, based on that I decided on merge. I created volcano plots to determine what kind of cut-off I should use in QC. I also made the Elbow plot to choose the dims. I am now looking at the UMAP (I used SCT normalization) and trying to choose the resolution. Do you have any advice on what I should pay special attention to?
I used SCT for normalization and then run FindAllMarkers + FindMarkers, as well as NormalizeData and bulkDE. I’m looking mainly at the log2FC to check if the trends are similar.
Has anyone ever done such an analysis? It’s only exploratory and meant to observe trends, but I still want to do it as well as possible. I’d appreciate any advice or thoughts on this, I think it will also be a valuable lesson for the future when we decide to sequence more samples.
Thank you for your time, Mery
