Hi,
I am running NMF/Consensus Clustering on my cancer samples and wanted it to cluster the samples into various subgroups, my question is how to conduct cluster assessment? Can I get P-value or something like that so that I can say my clustered samples are fine and validated?
Regards,
Dave
As mentioned by Kevin, there are many ways of scoring the quality of a clustering result and none is perfect as they generally make some assumptions about either the structure of the data and/or what a good clustering should be. In many cases, what represents a good value for the score is not always easy to assess. However they can be useful in deciding between different clusterings. Ultimately what matters is how relevant/interpretable the outcome is. For example, you may get a very good clustering by some measure but you'll find that its granularity is too fine, for example splitting what you consider should be one group into two. Ideally, you want your clustering to give you some insight into the biological question you're interested in and maybe generate some hypothesis that you can then test independently (either by looking at the data differently or by doing an experiment).