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?
Hi,
When I apply
sctransformwithbatch_var = "Batch"andlatent_varas default, the model becomesy ~ (log_umi) : Batch + Batch + 0However, thecorrectfunction currently only setslatent_var(i.e. log_umi) to its median value without touchingBatch. In this way, the corrected UMI seems to still contain the batch effect inside. I am wonder whether it makes sense to setBatchto the same level as well (e.g. for aBatchcontains values of "A", "B" and "C", set all samples to "B") right before buildingregressor_data? Is this going to give me a corrected UMI matrix without Batch effect?Thanks a lot!