Hi everyone,
I have some doubts about the removeBatchEffect function from the Limma package.
I am working on association of expression data (RNAseq) with a continuous phenotype variation (instead of a case control experiment), and I am using this function to remove the batch effect.
Can I use the values for my continuous phenotype in the design matrix?
The model I used so far was:
design= model.matrix(~ as.numeric(phenotype))
mRNA.nobacth = removeBatchEffect(Expr.mRNA, batch = batch1, batch2 = batch2 covariates = cov,
design= design)
Do you think this would introduce any bias to my analysis?