I have a question regarding the RMA normalisation for microarray data I came across on GEO. The expression data is related to toxic compounds. There are 200 compounds but for my analysis I only want to use 10 compounds. So, in this case do I need to normalise all the samples corresponding to 200 compounds or only the group of samples corresponding to the 10 compounds I want to make use of? It is really confusing. Please help.