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batch_var is not corrected in sctransform::correct #125

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dg520 opened this issue Jan 18, 2022 · 0 comments
Open

batch_var is not corrected in sctransform::correct #125

dg520 opened this issue Jan 18, 2022 · 0 comments

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@dg520
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dg520 commented Jan 18, 2022

Hi,

When I apply sctransform with batch_var = "Batch" and latent_var as default, the model becomes y ~ (log_umi) : Batch + Batch + 0
However, the correct function currently only sets latent_var (i.e. log_umi) to its median value without touching Batch. In this way, the corrected UMI seems to still contain the batch effect inside.
I am wonder whether it makes sense to set Batch to the same level as well (e.g. for a Batch contains values of "A", "B" and "C", set all samples to "B") right before building regressor_data? Is this going to give me a corrected UMI matrix without Batch effect?

Thanks a lot!

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