Dear All,

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?

Best,

K

Firstly, reply to answers using the "add comment" form, not the "add answer" form, unless you're answering your own question. Secondly, the "differences of differences" test can be done like this:

... where each term represents the log-expression of the corresponding group. The idea, as the mathematical expression above suggests, is to look for differences in the organoid/tumour log-fold change between the old and new batches. Of course, this is only applicable for DE analyses where you actually have two batches of organoid/tumour samples (and presumably the second batch is biologically different from the first, otherwise the difference of differences wouldn't be particularly interesting).