Question: ERR: Perplexity is too large in Reducedimension step in Monocle
9 months ago by
sciencer • 70
sciencer • 70 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.
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