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linnarsson-lab / adult-human-brain

Cytograph version used for adult human-brain analysis
BSD 2-Clause "Simplified" License
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Possible mismatch in google drive h5ad file and CellXGene h5ad #7

Closed jzleea closed 1 year ago

jzleea commented 1 year ago

Hi Linnarsson lab Thanks for this large body of work. I was reviewing the google drive linked h5ad files and I couldn't get the annotations to match what I also downloaded in h5ad format from the CellXGene resource. It is almost as if the neuron file and non-neuron file had some annotations swapped. Tsne and UMAP coordinates appear to match the papers though.

Data obtained from CellXGene (Non-neuron supercluster) image

Data obtained from google drive (Nonneuron.h5ad) image

Could someone confirm for me this is the case? Thanks! Jackson

simonmfr commented 1 year ago

Same issue for me @jzleea

jdime commented 1 year ago

Same issue for me @jzleea.

slinnarsson commented 1 year ago

Hi & thanks for noticing. I'll look into it and figure out what's wrong. Neither look like "tissue IDs" but rather like supercluster labels.

pl-ki commented 1 year ago

There was a mistake in the mapping of cellId to clusterId in the file on google drive. Thanks for pointing this out.