Open HelloWorldLTY opened 2 years ago
Hi,
20 PCs capture the most variances within used datasets, that's why we used this number of dimensions. For your dataset, I suggest you to run JackStraw function, JackStrawPlot and ElbowPlot as an example in this link to determine the number of significant PCs in your data, and extract these PCs vectors for your downstream analysis.
https://satijalab.org/seurat/archive/v3.0/pbmc3k_tutorial.html
Best, Hoa Tran
Ok, thanks a lot!
call_seurat3 <- function(batch_list, batch_label, celltype_label, npcs = 20, plotout_dir = "", saveout_dir = "", outfilename_prefix = "", visualize = T, save_obj = T)
Sorry to disturb you, but I wonder why I need to set npcs as 20 in this step, to run Seurat v3, because the default value of this step is 30. Thanks.