Find out which values are duplicates with the duplicated() function and then change them.

One question here is why are you having duplicated names? What does it mean? And, what to do with them? For example, if you are having duplicated gene names, so you have several rows containing information for the same gene, you may want to keep just one, and then Devon's solution is the way to go. Or, you may want to aggregate the results, computing, e.g. the mean value of the gene's expression in each sample. This will end also in unique names.