I tried to study as much as I could about the matter but I'm still confused. I have an Illumina Human HT-12 v4 expression data from our lab's RNA samples. I would like to see if I can combine the dataset with one I downloaded from GEO, also an HT-12 v4, to see differentially expressed genes between our cells and theirs. I would like to ask, what is the correct workflow for this kind of analysis? Can the following be applied?
1. read Dataset1 with lumi, do vst, rsn
2. read Dataset2 with lumi, do vst, rsn
3. combine both using function "combine" based on common features
4. remove batch effect using ComBat
5. do the actual differential expression analysis in limma
Does the process cover all that is needed? Or does a more sophisticated method for combining need to be implemented? I'd like to have confidence in the analysis results.