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
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
mean_contrast
outputs a vector of comparisons that I want to make:However, running this code gives the error:
Best wishes,
Jian