Open Sophia409 opened 2 years ago
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!
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(object@logupx.data[obj@var.genes,]))
to identify them and then subset them out of your data -- usually it is just one or two cells.
Hello, I have just started to use URD. I create an URD object by fetching data from Seurat3. But I got the following error when I run calcTsne and calcDM:
First error is 'Remove duplicates before running TSNE'.But After checking my data, I didn't find duplicated genes or cell names. Second error is : 'Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent', I searched this question many times but didn't find the reason.
It would be great if anyone has ideas about how to fix this error. Thanks. @farrellja @zouter @maximilianh