getGEO function is a way of getting datasets and their annotations from GEO in R when we want to analyze microarray data. GEO2R uses this function to get datasets. I saw in the GEO2R scripts of many of GEO cases that the tool does not perform background correction and substitution of duplicates with mean values anymore. I thought maybe it should be because of the use of getGEO. In other words, whenever we obtain datasets of GEO by using getGEO function, the data are background corrected and duplicates are substituted with mean, is it true? If it is ok, So, if we want to have our analyze by R (without GEO2R), if we get datasets through this function there is no need for background correction and substitution of duplicates with the mean anymore?