Only 9 features were used for prediction about celltypist

[ChuanXu1]

@B-WingBreaker, the immune model is from human, so very few genes are overlapped with your mouse data.

You can convert the human model to mouse one, and then apply CellTypist using the new model.

model = celltypist.Model.load('Immune_All_Low.pkl')
model.convert()
model.write('transformed_mouse_immune_model.pkl')
celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)

The result should be interpreted with caution due to inter-species difference.

[B-WingBreaker]

@B-WingBreaker, the immune model is from human, so very few genes are overlapped with your mouse data.

You can convert the human model to mouse one, and then apply CellTypist using the new model.

model = celltypist.Model.load('Immune_All_Low.pkl') model.convert() model.write('transformed_mouse_immune_model.pkl') celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)

The result should be interpreted with caution due to inter-species difference.

@ChuanXu1
This solved my problem well.
Most of the predictions seemed to match my preliminary annotation.
Thank you very much, ChuanXu1!

[Ahmedalaraby20]

I ran model.convert()
and I got AttributeError` type object 'Model' has no attribute 'convert'
Did something change ?

[ChuanXu1]

@Ahmedalaraby20, can you confirm your version by celltypist.__version__?

[Ahmedalaraby20]

its '0.1.9'

import celltypist
from celltypist import models
model = celltypist.Model.load('Immune_All_Low.pkl')
model.convert()
model.write('transformed_mouse_immune_model.pkl')
celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)

Am I doing it wrong?

[ChuanXu1]

@Ahmedalaraby20, this version is a bit old. Please try upgrading it by uninstalling and then installing a new one.

[Jammm11]

@B-WingBreaker, the immune model is from human, so very few genes are overlapped with your mouse data.

You can convert the human model to mouse one, and then apply CellTypist using the new model.

model = celltypist.Model.load('Immune_All_Low.pkl') model.convert() model.write('transformed_mouse_immune_model.pkl') celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)

The result should be interpreted with caution due to inter-species difference.

Could you tell me the corresponding Linux command? I have not used python. Thank you very much!

[ChuanXu1]

@B-WingBreaker, the immune model is from human, so very few genes are overlapped with your mouse data.
You can convert the human model to mouse one, and then apply CellTypist using the new model.
model = celltypist.Model.load('Immune_All_Low.pkl') model.convert() model.write('transformed_mouse_immune_model.pkl') celltypist.annotate(your_adata, model = 'transformed_mouse_immune_model.pkl', majority_voting = True)
The result should be interpreted with caution due to inter-species difference.

Could you tell me the corresponding Linux command? I have not used python. Thank you very much!

Cross-species model conversion is not possible with Linux command; you have to use the python code unfortunately.