batch_var doesn't work with vst.flavor = 'v2'

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

GNU General Public License v3.0

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batch_var doesn't work with vst.flavor = 'v2' #126

Open cnk113 opened 2 years ago

cnk113 commented 2 years ago

Hello,

When I set vst.flavor = 'v2' and batch_var between two different batches I get: Error in fit$Beta[, "Intercept"] : subscript out of bounds

Thanks, Chang

saketkc commented 2 years ago

The current implementation of vst.flavor does not support batch_var and will be added in a future release.

blasks commented 1 year ago

I'm wondering what the latest on this development is? Are there currently any workarounds to use the method = glmGamPoi_offset and exclude_poisson = TRUE options with batch correction?

Thanks for the great method!