Hi, I am following this tutorial " Integration and label transfer with Tabula Muris" Integration and label transfer with Tabula Muris - scvi-tools on SCVI-tools docs page and everything works fine and I save the predicted labels in the new metadata column
adata.obs[“C_scANVI”] = lvae.predict(adata) #saving predicted labels in new column
However when I check the ref labels, some of them are predicted differently than what it was before I trained SCVI model (when I concatenated with my query data).
I don’t understand why this is?
My understanding is that I am training the SCVI model on ref labelled data and then using SCANVI to transfer the labels on ‘unknown’ labels in query dataset.
Why is it predicting some of the ref data labels wrongly?
Any advise please. Am I doing something wrong here?
As you can see in the screenshot the ref data cell label ‘Cell cycle_TCGGTCTGTGAGAGGG-1_32_1-1’ is changed from Trm-c to CTL-c.