Hi, I don't know how to update the progress bar during the clustering calculation, I will check whether I can do anything.
The colours of the plot are assigned using the same rules than with PCA alone. In fact I use the same class (ProjectionPlotRenderer). 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? I am going to work on the help files now. Sandra ________________________________________ From: Tomas Pluskal [plus...@oist.jp] Sent: 24 January 2011 03:41 To: Developer discussion Subject: Re: [Mzmine-devel] Clustering module Hi Sandra, It looks good :) The progress bar does not update during calculation, can that be fixed? Also, what is the key to assign the colors in the final plot? Are you going to keep the current PCA and Sammons projection modules, or should these be removed? Tomas On Jan 21, 2011, at 5:25 PM, Castillo Sandra wrote: > Hi, > I have finished the clustering module using Weka library. What do you think? > Sandra > ------------------------------------------------------------------------------ > 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 > =============================================== 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 ------------------------------------------------------------------------------ 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
