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Scott Tyler (@ScienceScottT@genomic.social) Profile picture
Scott Tyler (@ScienceScottT@genomic.social)
@ScienceScottT
Developing new single cell omics methods and bench validating all the hypotheses those techniques give us. Opinions expressed are my own.
Jul 28, 2023 • 11 tweets • 3 min read
Yes, tSNE and UMAP overfit the data creating the impression of structure from nothing (even with 1000 obs & 200 features, not 2 -> 2). I don't have a twitter 'team' that I'm fighting for/against, but I had a hypothesis, tested it, and I'm just reporting the results... Image From the above, you're thinking: this is 2->2. It's not. It's using 2 "main" dimensions + noise in 100 others. Here's the actual inputs, and an example correlation of the input matrices: Image
Dec 9, 2022 • 20 tweets • 10 min read
Doing #SingleCell #RNAseq? Ever wonder if all those clusters are real? Turns out most feature selection & clustering pipelines can't tell when there's only 1 cluster! But I found a solution! 🧵👇 Happy to release (and welcome feedback!) on my new feature selection algorithm that can help prevent false discoveries in scRNAseq datasets! bitbucket.org/scottyler892/a… (pip installable & works easily with scanpy :-) @fabian_theis