LTLA
commented
3 years ago There is no restriction on the number of cells that can be supplied to SingleR - the examples in the book frequently use more than 800 cells. I don't know what facy_mseq is, either; no such variable exists in the SingleR code base.
Create a minimum reproducible example, then we might make some progress. The code snippet you've provided has obvious problems so it's hard to know what you did wrong. Why do you assign to mtsx but then use test = mtx? What's in the rest of the SingleR() function call, given that you didn't show the closing parentheses?
j-andrews7
my code is like
mtsx = seurat.obj@assay$RNA@data[, 1:800] ref.data = HumanPrimaryCellAtlasData() pred = SingleR(test = mtx, assay.type.test=1, ref=ref.data, labels = ref.data$label.main
When more than 800 cells: Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'flesh' in selecting a method for function 'relist': object 'facy_mseq' not found.
When less than 800 cells, I got DataFrame with likely correct results with columns scores, first.labels, tuning.scores, labels, and pruned.labels.
Any suggestion?