I am planning to work with the gene expression data of T2DM from several different experiments that include several groups within them (all of them are from the same platform though i.e, Affymetrix), to get the differentially expressed genes using Bioconductor packages. However, I am unsure of which approach to use for this analysis. I was planning to get the DEGs from individual datasets separately and then find the common DEGs across the different datasets. Is this a correct approach for this type of analysis? Or do I need to merge the datasets into a single Expression Matrix and go ahead from there?
Thanks in advance!