I am analysing a gene expression profiling (Illumina microarray) of 12 samples, 6 of them are organoids and 6 are the matched tumor samples. The gene expression profiles of organoids and tumor samples look different and I identified hundreds of genes differentially expressed (lmfit+eBayes+topTable, adj-p-value < 0.05). The goal of my project is not to identify difference between organoids and tumor samples but to get the two profiles comparable. I was thinking to use removeBathEffect of limma using Organoids and WT as a batch and correct for this know source of variation. The question is: is it possible to re-use the same beta coefficients calculate by the removeBatchEffect function and apply them to a new set of organoids samples profiled with the same platform?