Hello everyone, I am relatively new in this field and I have different expression data sets from GEO. I am working on downloading them to R, pre-process and analyze. I found many different methods like RMA but I am not sure which one should I use. I want to use a simple method to build a script for all data sets. The simples methods are these: http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html (in the middle of page) http://felixfan.github.io/RMA-Normalization-Microarray/
Are those methods enough for normalization and good to use? What other methods do you advice? Should I change my methods depending on my data sets? My datas are all from Illumina HiSeq 2500 platform. I think I should not use Affy package for this. Thank you.