I am working with few microarray datasets for DEG analysis. I have downloaded the raw data and doing normalization on my own. Some of the datasets I have can be subdivided into groups based on their phenotype (each group include case and controls). I am using Bioconductor packages for this analysis. I understand that during the DEG estimation (using limma) I need to have these groups as separate expression matrices. However, I am not sure if I can normalize the whole dataset (using RMA) and then subdivide the samples into groups or Do I need to separate out the groups from the parent dataset before I do the normalization process? Do the final results vary between these approaches?
Thanks in advance!