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Why annotation results are totally not correct #11
Description
I used GSE115600 for example, which were LogNormalized before runing AzimuthAPI.
However, the annotation results were totally not correct. All the neural cells were annotated as immune cells.
table(sc$Cell_type,sc$full_hierarchical_labels)
Immune cell|Lymphoid cell|T/NK cell|T cell|CD4 T cell|Naive CD4 T cell
aNSC1 609
aNSC0 452
qNSC1 450
aNSC2 382
qNSC2 315
NB 298
TAP 435
OD 83
OPC 44
table(sc$azimuth_broad)
False Immune cell
3052 16
I wonder how can this package be accurately applied for our own data?
Activity
DarioS commentedon Jul 29, 2026
GSE115600 is of Mus musculus, not human.
I just made the same mistake. I hope that they will offer a model for mouse in the future.