I have a collection of numeric quantitative variables from a series of samples; let’s say, for example, countries from the whole world. My goal is to discern how countries can be distributed, according to these variables, into classes by using k-means. But I am interested only about the results concerning European countries (always as an example), that is, how European countries alone distribute into classes.
So, my question is, do I perform the kmeans analysis taking into account only the European countries, and discarding from the beginning the other countries?
Or is it better to perform first the kmeans analysis including all the world countries, and describe afterwards the results concerning the European countries? - assuming that the European countries do not appear all within the same cluster-.
Just to enter into details, the quantitative variables are gene expression data (4000 genes); and the “European countries”/samples are selected brain regions (in number of 400) from a total of 1000 brain regions.