I am trying to run {Rtsne}. On pca
dataset prepared by using dudi.pca
from {ade4}.
For pca calculation I selected 40 components while specifying parameters for dudi.pca
:
pca = dudi.pca(counts(sce_normalized), scannf=FALSE, nf=40)
{Rtsne} gives me an error: “perplexity is too large”, how could it be fixed?
The code I am trying to run is below:
name_of_file <- "dudi_pca.rds"
path_to_file <- paste0("/scratch/nv4e/scRNA-
seq/normalization/new_datasets/",
name_of_file, sep="")
dudi_pca <- readRDS(path_to_file)
# run Rtsne with default parameters
rtsne_out <- Rtsne(as.matrix(dudi_pca), pca=FALSE)
dudi_pca
? $\endgroup$20 000 x 40
$\endgroup$