I have a data set of 54000 genes and I used different methods for clustering such as HAC, K-means, model based clustering and CLARA. The objective is to compare these methods. I used the Adjusted Rand Index. But there is something that I do not understand.
With my data set, the ARI value between a clustering result obtained by K-means and another clustering result, also obtained by K-means, with the same number of clusters (i.e I effectuated K-means two times) , is only 0.40, which is not a high value.
My question is, if the ARI value is not high for the same method compare to itself, can we use ARI to compare the clustering results for different method? And is there other index or method to compare them? I already read the topic How to select a clustering method? How to validate a cluster solution (to warrant the method choice)? but I still do not understand which methods are used to compare the clustering results.