kmeans error when running reduceDimension(reduction_method = 'DDRTree')
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Entering edit mode
3.4 years ago
mk ▴ 210

After setting my ordering filter, I run:

colonTumor <- reduceDimension(colonTumor, max_components = 3, norm_method = c("none"), reduction_method = 'DDRTree', verbose=TRUE)

Then I get the following error:

Error in kmeans(t(Z), K, centers = centers) : initial centers are not distinct

Here is some info about the data I have used to create the CellDataSet:

Browse[2]> str(colonTumor@assayData$exprs) Formal class 'dgCMatrix' [package "Matrix"] with 6 slots ..@ i : int [1:9499265] 2 5 14 15 23 24 27 29 30 31 ... ..@ p : int [1:1905] 0 5478 11248 15546 21080 24719 28635 32894 38503 42469 ... ..@ Dim : int [1:2] 19326 1904 ..@ Dimnames:List of 2 .. ..$ : chr [1:19326] "RP11-34P13.7" "FO538757.2" "AP006222.2" "RP4-669L17.10" ... .. ..$ : chr [1:1904] "Edge1_AAACGGGGTACCGTTA" "Edge1_AAACGGGTCTGGCGAC" "Edge1_AAAGATGAGCCTCGTG" "Edge1_AAAGCAAAGACTGTAA" ... ..@ x : num [1:9499265] 4 1 6 6 5 2 1 1 1 4 ... ..@ factors : list()

monocle irlba kmeans ddrtree • 1.2k views
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Entering edit mode
3.4 years ago

Something is weird about your dataset... it's too 'flat', i.e., lacking in structure or something along these lines.

This error was additionally reported on GitHub and the developer responded: kmeans centers not distinct in new DDRTree version #26.

Please try the suggestions.

Kevin

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