Question: ERR: Perplexity is too large in Reducedimension step in Monocle
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8 days ago by
sciencer0 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 • 64 views
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