Question: ERR: Perplexity is too large in Reducedimension step in Monocle
gravatar for sciencer
9 months ago by
sciencer70 wrote:


In reduce-dimension step while Clustering cells using marker genes in Monocle, I get the following error, acn anyone help, I am new to R, Please!

HSMM <- reduceDimension(HSMM, max_components = 2, norm_method = c("log"), reduction_method = c ("tSNE"),  verbose = T)
Remove noise by PCA ...
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.
Reduce dimension by tSNE ...
Error in Rtsne.default(as.matrix(topDim_pca), dims = max_components, pca = F,  : 
  Perplexity is too large.
rna-seq R software error • 976 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by sciencer70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1662 users visited in the last hour