Hello,
I am trying to generate a Tsne plot to look at the distribution of different TFs between clusters as in the chromVAR vignette. However, whenever I run deviationsTsne, I get this warning
tsne_results <- deviationsTsne(dev, threshold = 1.5, perplexity = 10,
shiny = FALSE)
Error in Rtsne.default(t(mat[ix2, , drop = FALSE]), perplexity = perplexity, :
Remove duplicates before running TSNE.
I tried looking at the matrix manually and removing motifs with duplicate expression and then rerunning from matchMotifs(), however, am still getting the same error even though I can no longer identify duplicates in my assays(dev)$deviations object. I am also able to make a Tsne manually using Rtsne(), but would love to play with the shiny output that is incorporated in your vignette. Any ideas on how to go about addressing this? Thank you.
Hello,
I am trying to generate a Tsne plot to look at the distribution of different TFs between clusters as in the chromVAR vignette. However, whenever I run deviationsTsne, I get this warning
I tried looking at the matrix manually and removing motifs with duplicate expression and then rerunning from matchMotifs(), however, am still getting the same error even though I can no longer identify duplicates in my assays(dev)$deviations object. I am also able to make a Tsne manually using Rtsne(), but would love to play with the shiny output that is incorporated in your vignette. Any ideas on how to go about addressing this? Thank you.