question in reduceDimension

[Shawn10312]

Want to use monocle2 to show the trajectory. But in the plot_pc_variance_explained , it showed the warning, and I can not make sure how many pc are explained. So I set the parameter num_dim = 10 in the run of reduceDimension, and I confront the error as the following. But when num_dim = 2 was setted, it can run.

Anyway, I want to know, whether there is a error in the upstream analysis? Or never mind.

> plot_pc_variance_explained(monocle_malignant, return_all = F)
Warning message:
Removed 100 rows containing missing values (geom_point).

> monocle_malignant <- reduceDimension(monocle_malignant,
+                                      max_components = 2, num_dim = 4,
+                                      reduction_method = 'tSNE',
+                                      residualModelFormulaStr = "~num_genes_expressed",
+                                      verbose = T)
Removing batch effects
Remove noise by PCA ...
Reduce dimension by tSNE ...
Error in Rtsne.default(as.matrix(topDim_pca), dims = max_components, pca = F,  :
  Remove duplicates before running TSNE.

[davidT0712]

have you solve your problem?I encountered the same problem

[qqxj]

我也遇到了这个问题，请问大神如何解决呀