I have integrated multiple datasets successfully using fastMNN. I am now needing to subset the data to focus on the analysis of specific clusters. My questions are as follows:
Is it recommended that I rerun the fastMNN integration again on the subsetted data? Would it be appropriate to use subsetted corrected PCA dimensions done from the first round of integration for dimensional reduction? In other discussion threads that have discussed integration such as Seurat's CCA, it is not recommended to rerun the integration if an integrated dataset is subsetted. However, Seurat conducts the correction in the gene expression space versus the PCA space like fastMNN so it is unclear to me what the best approach should be.
Any advice would be greatly appreciated!