I used GEO2R to find the list of differential expressed genes between cancer and normal tissue.
I did not know the expression of which group(cancer or normal) is divided on the other group.
I found a tutorial in which it had been said that the treated group must be defined first (indicated by blue in GEO2R).
However the results that I get is not in agreement with the previously reported up or down-regulation for most of genes.
Can anybody tell me what is the correct order of defining groups in GEO2R?
Thank you in advance