please may I ask for a suggestion :
I have a scRNA-seq dataset, which has 2 groups (Control and Model).
I would like to process all the samples into cluster by tSNE or UMAP , then classification or differentiation the cell types.
Which method should I choose?
- Method one: The model group and the control group were analyzed respectively.
- Method two: All the samples were analyzed together.
In my opinion, as there may be differences in gene expression between the two groups, it is necessary to analyze and identify cells separately. But many articles only provide one figure about tsne or cell classification, and I suspect that the method two is adopted.