For a project I reanalyse data from a study (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50395) in order to perform a Differential Gene Expression Analysis between 2 conditions (3 patients vs 3 controls).
My first idea was to use the software GEO2R because data values are already normalized signal intensity from the single-ship array.
But as you can see with the value distribution box-plots:
Values across samples aren't median-centered ..
My question is does GEO2R standardize theses values between the different samples or I have to normalize the data first? If I have to normalize the data, how to perform this normalization?
Thank you in advance for your help