Hi Sandra, > I don't think it is a good idea to remove PCA or Sammon's. In the context of > clustering, PCA or Sammons are just visualization tools (add ons) > but in general, you would like also to visualize the original clinical > grouping of samples. For clustering PCA visualization I only show the two > first components, removing the rest to simplify the parameters. > I have seen that the actual PCA method is not working for all the data sets. > We are developing (in my group) a new Java library for data analysis which > contains the NIPALS (Non-linear iterative partial least squares) method for > PCA which should work always. Should I change it?
Do you know what is the reason that the current PCA method does not work for all data sets? By the way, how about hierarchical clustering for the individual metabolites? :) Tomas =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
