Hi, I was wondering how to do downstream analysis for cells which are subsetted after MNN batch-correction. According to the OSCA, we can
repeating modelling and PCA on the subset.,and then we can do UMAP, cluster.
But this document is for one single cell data, I am confused about the the fastMNN integrated cells. Accoring to some issuses from Bioconductor support or github, I can do fastMNN or not. But I am still confused about some steps.
For the first step(model var), I am sure I have to model var again. But I am not sure how to model var. After all, these subseting cells from two or more scRNA-seq set. should I use the modelGeneVar with block factor to mar batchs?
For the second steps(PCA), should I use
corrected value from fastMNN or just
origin logcount ? should I do multiBatchNorm again?