Comments (4)
wangmeijiao
commented on August 23, 2024
Oh, I selected genes from the snRNA variable genes only, which is recommended.
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jw156605
commented on August 23, 2024
One thing to check is the reference dataset. By default liger uses the dataset with the largest number of cells as the reference during quantile normalization. But when aligning RNA and ATAC data, you should use the RNA dataset as the reference regardless of size.
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wangmeijiao
commented on August 23, 2024
Wow! that is definitely a good point! Thanks for the message. I will tell the 'quantile_norm' to use my snRNA data as reference.
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mvfki
commented on August 23, 2024
I've had Josh's recommendation addressed in a way that reference will be automatically chosen from an RNA dataset if the modalities is properly set when creating a liger object, and a warning will be issued when the reference chosen is of other modalities. This is now available in master branch and will be on CRAN hopefully next week.
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Related Issues (20)
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- log transform data first? HOT 1
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- Prepare for upcoming Seurat v5 release HOT 1
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