Comments (2)
jsnagai
commented on May 18, 2024
1
@qiuhuiqq Did you feed the PCA matrix to PHATE instead of the raw count matrix? When i did it in my end, i could retrieve pretty close results compared to RunPHATE.
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scottgigante
commented on May 18, 2024
Without having run this myself and looked in detail, the first thing that jumps out at me is that Seurat does not use the sqrt transformation. What do the results look like for the two different PHATE plots? If you apply a log transform in the second version in place of the sqrt transform, what does it look like then?
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Related Issues (20)
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