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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Zero score when annotate new visium dataset using a reference #9450

Open Chrisdoan9 opened 2 weeks ago

Chrisdoan9 commented 2 weeks ago

Hi all,

I try to follow the tutorial on cell annotation for visium data https://satijalab.org/seurat/articles/spatial_vignette. However, I got zero score for many cell types should have in brain. Would you please suggest possible reason for this? Thank you! Screenshot 2024-11-02 at 11 57 13 AM

zskylarli commented 1 week ago

Hi - what reference are you using to transfer labels from? Additionally, are you finding enough anchors between your query and reference when you are running FindTransferAnchors (a message should show in your session giving the number of anchors)?

Chrisdoan9 commented 1 week ago

HI @zskylarli, I use Allen reference data with 166,868 single nuclei which has these cell types: Pax6, L5/6 NP, L5 IT, L6 CT, L4 IT, Astrocyte, L2/3 IT, Vip, Sst Chodl, L6 IT Car3, L6 IT, Sncg, Pvalb, Oligodendrocyte, Lamp5 Lhx6, Sst, VLMC, Lamp5, Microglia-PVM, OPC, L6b, Endothelial, L5 ET, Chandelier, max. FindTransferAnchors() I have 413 anchors. Neuronal cell types such as L2/3 IT, L4 IT has no signal which mean somethings went wrong. I rerun the analysis and the cell types in bold has signal. Thank you for your suggestion. image https://portal.brain-map.org/atlases-and-data/rnaseq/human-mtg-10x_sea-ad

Chrisdoan9 commented 1 day ago

This paper developed a method for cell type deconvolution: https://pmc.ncbi.nlm.nih.gov/articles/PMC10692090/ Not sure how accurate the method seurat used compare with other methods.