kmeans enrichment vs kmeans raw and others....

[Petros Kolovos]

Dear All,

I have a pretty much basic question.....

I am using as reference data one chip-seq file and I am 'alligning' with other 3-4 chip-seq files.

In the clustering normalization, what is the best method to use?

Because with the same kmeans seed and the same number of clusters, i see differences when comparing Kmeans raw to Kmeans enrichment...

Could you please give us some basic guides on when we should use each different way of normalization?

Thank you in advance

Best
Petros