Hi Chris & Mark, Thank you very much for the testing and reports! I am still working on fixing the bugs and glitches caused by the changes in the underlying framework. I think you don't need to submit these issues into the bug tracker at the moment, I will go through them and let you know when they are all fixed.
> > The peak detection now seems to be split into several steps. When I > generate a mass list it seems to calculate something but then no mass list > appears in the list so I can’t proceed with the peak detection. The mass list appears in each individual scan. If you roll open the data file in the project tree (left part of the window), you will see that scans now can be rolled open, too, and from each scan you can open the mass lists associated with that scan (there can be more than one). I know this is a bit cumbersome, so please let me know if you have a better idea about how to represent the mass lists in the project tree. You can proceed with the peak detection by running either mass list filter or chromatogram builder, both of which take a mass list name as a parameter. > The Mass detector Wavelet transform “Show Preview” does not work and there > are no default values in the boxes any more. The Wavelet window size every > time you enter a value and click on the show preview it clears the box. Actually, the preview works, but it throws an exception in case the parameter values were not specified correctly. I will check about that. I will comment about the missing default values further below. The window size value can be inserted as "30%" but not "30". I will fix that, too. > The Mass detector Recursive threshold function works up until you click OK > then I get a “Unhandled exception in task Detecting masses in QC5_917_19.RAW > java.lang.ArrayIndexOutofBoundsException I would like to see the messages of the MZmine console window, to find where exactly the exception occured. Or you can send me the raw file and what parameters you used, so I can identify the problem. > The mass detector Local maximum seems to work but no mass lists are > generated > The mass detector Exact mass and Centroid appear to do nothing. The resulting mass lists can be found as I wrote above. > > So basically I can’t progress any further past this stage to do the peak > detection. Opening a previously processed file I have tested some of the > later functionality: > > Joining peak lists: Again all boxes are clear with no default values which > makes it hard for a beginner. I removed the default values on purpose. The default values had no real meaning, actually. The parameter values always need to be adjusted according to the characteristics of your data. We have been getting too many messages from users who always say "MZmine does not detect any peaks, what is the problem?" and the problem is always the same - they rely on the default parameter values and do not change them. When we remove the default values, users will be forced to think about each parameter and understand what they are doing. Of course, once you enter a value, it will be remembered, so you do not need to think about it again. As for beginners - they need to read the manual/help, and removing the default values will force them to do it. > There is no help for the new option path aligner The path aligner is an experimental module made by Sandra, I am not sure if it will be actually included in MZmine. > Crucially the Identification/Online Database search no longer seems to > search the whole peak list. You have to manually enter a mz value. That is a bug, will fix that. > It seems to refuse to save the peaks list as a .CSV file What do you mean by refuse? Anyway, I will check it. > How do you enter the standard compounds for the new retention time > normalisation step? That is a bug, will fix that. Give me a bit more time :) Best regards, Tomas ------------------------------------------------------------------------------ BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-attend event for mobile developers. Connect with experts. Get tools for creating Super Apps. See the latest technologies. Sessions, hands-on labs, demos & much more. Register early & save! http://p.sf.net/sfu/rim-blackberry-1 _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
