The proposed analytical tool yielded meaningful comparison of the two corpora; in addition, it has proved to be more reliable than previous analyses of cohesive reference. However, what has not been mentioned so far is that inconsistencies were sometimes due to various kinds of reference errors in the research papers, especially in the MA theses. While problematic items were marked by the coders, some of them were left out or categorized as belonging to the category intended by the writer. The type of error and the instances these occur were noted during the analysis. The question of how to deal with these problematic items to describe reference in student writing is explored in detail at Stage 4 (in Section 6.4), leading to the final analytical tool as the last stage of our empirical studies.