Hello, I want to use SC3 for data sets from multiple batches. I use fastMNN() function of Scran/Scater package for batch normalization but it does not effect logcounts, it creates a reduced dimension "MNN" that shows the corrected data which also used in clustering step. How can I use SC3 with these values? Can I create a new SingleCellExperiment with MNN matrix and use SC3 on that matrix? MNN matrix includes negative values so I know I should not use gene_filter parameter as TRUE.
Thank you in advance.