celltypist before/after batch correction

[malonzm1]

Hi,

I perform batch correction using scVI. But I perform celltypist prediction before batch correction. Is it better to perform celltypist after batch correction or it doesn't matter?

Good day.

[ChuanXu1]

@malonzm1, predicted_labels is only dependent on gene expression matrix, but majority_voting will be influenced by the neighborhood graph if it is constructed from scVI latent space.

[malonzm1]

Thanks!

[malonzm1]

Is majority_voting more reliable if celltypist is run after batch correction?

[ChuanXu1]

@malonzm1, depends, but majority_voting is usually more readable.

[smallsmalltown]

@ChuanXu1 Based on what you've described, it seems that batch effects will not impact the predicted_labels, but they can influence the majority_voting results??? After applying harmony to remove batch effects, my data also encountered the issue of "Invalid expression matrix in .X, expect log1p normalized expression to 10000 counts per cell; will use .raw.X instead."

[ChuanXu1]

@smallsmalltown, as I remember, Harmony will not change the expression values but produce only the corrected latent space. To predict your data using CellTypist, you need to provide a normalized gene expression in either .X or .raw.X.