While following the Batch Alignment walk-through, found that prep.cytonorm function does not keep original cell marker columns (cellular.cols) even when specifying to keep both the original and coarse aligned columns ( cellular.cols = c(cellular.cols, paste0(cellular.cols, crs.append)) ).
I am clustering by the coarse aligned cell makers ( paste0(cellular.cols, crs.append) ), this impacts several down-stream commands which require the original column names (e.g. train.cytonorm & run.cytonorm)
While following the Batch Alignment walk-through, found that prep.cytonorm function does not keep original cell marker columns (cellular.cols) even when specifying to keep both the original and coarse aligned columns ( cellular.cols = c(cellular.cols, paste0(cellular.cols, crs.append)) ).
I am clustering by the coarse aligned cell makers ( paste0(cellular.cols, crs.append) ), this impacts several down-stream commands which require the original column names (e.g. train.cytonorm & run.cytonorm)
Thanks in advance