How to interpret a tSNE or UMAP plot to get biological conclusions ?
Hello all,
Would you please tell me how to interpret a tSNE or UMAP plot to get biological conclusions? I read some scRNA-Seq analysis but still haven't gotten the biological meaning of these plots. Thank you so much!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937596/ Figure 6 of this paper is a sample.
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bardarjoki •
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Chris •
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Chris •
1 answer
Here's one take on them:
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In general, tSNE or uMAP are just methods to cluster the data to diffrent clusters. Afterwarwds you can check which genes/markers each cluster are consist of, and then devide the general cell vluster to smaller vlusters, which each defined by unique markers (gene expression/etc.)
Thank you for your reply!
That is not technically correct. Community detection algorithms are used to generate clusters. tSNE and UMAP are dimensionality reduction algorithms.
Would you please clarify which not technically correct is?
"tSNE or uMAP are just methods to cluster the data" is not correct. They are dimensionality reduction algorithms.