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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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SCTransform error when using batch or other latent variables #88

Closed kmwinkley closed 3 years ago

kmwinkley commented 3 years ago

When using a batch variable in SCTransform, the error:

Error in is.nan(rel_attr) : default method not implemented for type 'list'

appears. I believe this originates from the "is.nan" line in implemented in utils.R

rel_attr <- cell_attr[, c(latent_var, batch_var, latent_var_nonreg)] if (any(is.na(rel_attr)) || any(is.nan(rel_attr)) || any(is.infinite(rel_attr))) { stop('cell attributes cannot contain any NA, NaN, or infinite values') }

This error is not returned when performing SCTransform normalization on the same data without the batch variable.

ChristophH commented 3 years ago

Thank you for pointing this out. Fixed in the develop branch