Remove batch effect in test_differential_abundance

[jianwu1]

Hi @stemangiola ,

Can I ask how to remove batch effect for DE analysis using tidybulk? I try to include batch factor in the linear model for test_differential_abundance but the code gives error. I have a design matrix:

from which I want to do DE between different conditions, but want to remove batch effect considering the batch column

  test_differential_abundance(
   .formula = ~ 0 + condition + batch,
   .contrasts = mean_contrast(counts, condition),
   method = "edgeR_quasi_likelihood", 
   action = "only" )

mean_contrast outputs a vector of comparisons that I want to make:

However, running this code gives the error:

Best wishes,

Jian