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trucnguyen89 avatar trucnguyen89 commented on July 21, 2024

Hi,

I encountered the same error when running calcDM:
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent

I would be thankful if anyone suggests some solutions for this . Thanks so much!

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farrellja avatar farrellja commented on July 21, 2024

Hi @Sophia409 and @trucnguyen89
This is because calculating tSNE or a diffusion map fail if there are duplicate points. Not duplicates by name, but by coordinates (i.e. two cells in your data have the exact same expression values across all of the variable genes you're calculating on.). I will need to add a check for this in the URD functions. To get started immediately, you can identify them and remove them. Try duplicated(Matrix::t([email protected][[email protected],])) to identify them and then subset them out of your data -- usually it is just one or two cells.

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