Well there is no method or procedure which can be universally used to normalize the data as you are looking for.
Normalization is done for different samples/conditions within the data and not across or between multiple datasets. And that is what the paper mentioned above is dealing with. Normalization methodology for a data set.
Further, its not just the data sets are different, they are generated by different platform. Thus, in addition to the batch effect, there can be several other factors which should also be considered before normalization.