Dear all, I am following this discussion with great interest and I'd like to make a comment. As I am not BASE2 user, please ignore my comment if I got it wrong.
The trick used in BASE1 and apparently kept in BASE2 (ie import data such as test and ref samples associate consistently with the same channel, at least for a given experiment) is fine as long as you work with a sample vs ref design. But it won t work if you deviate from this design so in case one wants to do something a bit more "clever" at the plugin level, one must have access to the annotations associated with each label extract. Another thing is that users usually do *not* understand this ch1/ch2 trick. And simply making sure that data is loaded properly can be a nightmare. We solved this by implementing a web wizzard front end where users must specify right from the beginning if their experiment uses "dye swap design". In this case, the GUI enforces the hybridizations to be loaded as hyb couples. This way we automatically use the proper parser. I don t know if you have something similar in BASE2 ie loading "couples" of hybs (with the possibility to define pairs of loaders) but I am convinced this would be of great help and hide away the db logics. Cheers Charles On Nov 16, 2007, at 1:42 PM, Bob MacCallum wrote: > > > Nicklas Nordborg writes: >> I really don't see how a 'channel' attribute could help answer that >> question. Everything upstreams of the raw bioassay is generally >> speaking >> not accessible in the analysis module. The only upstreams information >> you can use are annotations that have been inherited to the raw >> bioassays and specified as experimental factors of the experiment. >> For a >> single raw bioassay this should be either 'male' or 'female'. The > > So even though the two samples/biosources each have an annotation > (one "male" > one "female"), you would recommend that the raw bioassay should > inherit only > from one. > > As discussed here: > http://www.mail-archive.com/[EMAIL PROTECTED]/ > msg00907.html > inheriting from more than one item leads to undefined behaviour. > > I'd like to suggest that one should be able to inherit annotations > from > multiple biosources in a defined order (e.g. ch1, ch2). > > Alternatively, some innate ordering of the labelled extracts with > respect to > hyb (again in channel order). > >> dye-swapped hybridization should be imported so that the 'male' >> channel >> is the same as for the one not dye-swapped. Then all your ratios >> can use >> the same formular. > > Yes I agree that the BASE1 approach (different import configs for > dye-swapped > hybs) is the way to avoid ratio mixups/complications during analysis. > > cheers, > Bob > > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel ===================================== Charles Girardot European Molecular Biology Laboratory C. Boulin and E. Furlong Groups Tel: +49-6221-387-8426 Email: [EMAIL PROTECTED] Meyerhofstrasse 1 - Postfach 10.2209 69012 Heidelberg, Germany ===================================== ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
