I did this & the # of genes changed the clusters but this is ++compute intensive. Anyone know of any good reviews now on params used for cell type clustering?
The cell type clustered affects any claim of this sort, I find that interesting, would be nice to know if anyone has written about it.
The cell type clustered affects any claim of this sort, I find that interesting, would be nice to know if anyone has written about it.
Reposted from
Daniel León-Periñán
This is from the Illumina #AGBT25 workshop about their ST tech.
But, from our observations, under heavy lateral diffusion (real or simulated), clustering on large sets of genes (i.e. “whole transcriptome”) leads to niche- rather than cell-type clustering.
This might be problematic.
But, from our observations, under heavy lateral diffusion (real or simulated), clustering on large sets of genes (i.e. “whole transcriptome”) leads to niche- rather than cell-type clustering.
This might be problematic.
Comments
One that gets close is the Hu et al 2024 (Genome Biology) meta-analysis, but they study niches, not cell types.
There are others about imaging-based data, but these are handled differently (bc of big differences in sensitivity).
https://pubmed.ncbi.nlm.nih.gov/38940162/