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?

Best wishes

Guandong Shang

Thanks for your reply, Aaron :)