tropy wrote: > Nicklas Nordborg wrote: >> tr...@valdelsa.net wrote: >> >>> 1. Log2 ratio transform
MeV behaved (still behaves) inconsistently with data it read from TDMS with respect to logging data or not. In some cases MeV auto-logged data and in some other cases it did not. When we began to integrate MeV with BASE we could not find any written documentation on when to expect MeV to log or not. So, we decided to always export non-logged values because this makes it easy for the user to understand what is exported from BASE, and if we always do the same export, then the user does not need to hesitate over what data was exported. The export could be modified but as Nicklas says, it is trivial to log the data in MeV, so currently I would vote against a change to exporting log2 ratios. >>> 2. Average on reporters (or by other Annotation Fields) >>> >> Average on reporters might be possible, but I don't see how annotations >> should be used in this context. In any case, it may be better to have >> 'merge' functionality as a separate plug-in step. I am not aware of any >> BASE 2 plug-ins for merging but there is at least one BASE 1 plug-in >> that can merge on annotations. >> >> > Yes, maybe the average on different annotations could be difficult to > implement and should be computed by a specific plugin. But the average > on reporters identifiers at least it's very important just to have the > same results that you can get from the BASEexporter plugin. There is a BASE1 plug-in that does merge on reporters, http://baseplugins.thep.lu.se/wiki/se.lu.onk.VirtualArray but it only works for 2-channel data (maybe it is easy to add 1-channel support?). Running the plug-in before starting MeV would give you the same data in MeV and a BASEfile export (for the bioassay set resulting from the VirtualArray). The TDMS export and BASEfile export are two different exports coming from two different sources. The BASEfile export is a part of the core BASE functionality whereas TDMS export is a part of the MeV extension package. One may hope for similar functionality but since they have different origin there is no guarantee for getting the same functionality. (I'll admit that Nicklas has implemented both exports.) I would rather see the average on reporter removed from the BASEfile export than introducing it for the other exports. The reason for this is that I'd like plug-ins and functions to do well defined task. BASEfile export should export data, not calculate averages. What is missing is a general average on reporter plug-in that can be used before exporting data. (I'll add that to the wish list of plug-ins.) >>> 3. Add the possibility to export raw data or formula columns also >>> >> I don't think this is possible with the TDMS format, since there can >> only be one value (eg. the intensity) for each spot. Unless you mean >> that a formula should be selected *instead* of the regular intensity. >> This would then also solve 1). > > Frequently it's necessary to have the possibility to export not only > ratios, but also different raw data columns or computed statistical > quantities. The TDMS format supports additional columns to the left of the actual data matrix and one could add raw data columns and other formula based information there. However, I do not think BASE supports statistical quantities over bioassays trivially (as needed here). How would you use such extra columns in the TDMS file? Can MeV calulate the statistical quantities if raw data and formula based columns were added to the export? > About this, if you're interested, I'll try to report to you (in a > different thread / email) our experience about the transition from BASE1 > to BASE2. I would be very interested since I get off-line questions regarding migration. Can you send it to the list for others to read and maybe find when they migrate. Which version of BASE2 did you migrate to? I have one facility that seems to have succesfully migrated to 2.12. Cheers, Jari ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
