Thanks very much Jari. Sorry I didn't have time to look deeper and figure out what was wrong. As you'll see in a few weeks we have a big project nearing release.
cheers, Bob. Jari Häkkinen writes: > Hi Bob, > > We are looking into the issue. It looks like the BASE2 version of lowess > is flawed. We are testing and reading publications to make sure that we > make a proper fix. We already have a fix for the problem but want to > make sure that we don't create new bugs. We plan to release a 2.7.2 ASAP > with the fix. > > Thank you for reporting this issue to us. > > > Jari > > > Bob MacCallum wrote: > > I've done some more tests on the lowess problem. > > > > Please refer from now on to our development server: > > > > http://base.vectorbase.org:8080/base2dev/ > > Experiment: "Male vs. female (Koutsos et al., 2007)" > > > > I ran the base1 lowess plugin and got a very different result compared to > > the > > base2 plugin. The base1 plugin results look correct to me. The base2 > > correction factor plots do not look at all right to me. > > > > Can anyone hazard a guess as to if this is a bug or are the default > > parameters > > not suitable for my data? > > > > Due to time pressures I think I'm going to have to switch all our analysis > > over to use the base1 plugin. > > > > many thanks, > > Bob. > > > > Bob MacCallum writes: > > > > > > Has anyone had problems with the Lowess analysis plugin? > > > > > > To me it looks like it is overcorrecting. Where a M/A plot > > > is largely below the zero line before normalisation, it ends > > > up largely above it afterwards. > > > > > > I'm using default values (including 0 for block group size). > > > Default values were always fine in BASE1. > > > > > > You can look for yourself with the guest login at > > > http://fungen.vectorbase.org/base2 > > > > > > Experiment "Male vs. female (Koutsos et al., 2007)" is a good > > > small example. > > > > > > I don't see a recent ticket on this (I have not upgraded in > > > a few months). > > > > > > cheers, > > > Bob. > > > > > > > > > -- > > > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > > > Division of Cell and Molecular Biology | Imperial College London | > > > Phone +442075941945 | Email [EMAIL PROTECTED] > > > > > > > > ------------------------------------------------------------------------- > > > Check out the new SourceForge.net Marketplace. > > > It's the best place to buy or sell services for > > > just about anything Open Source. > > > http://sourceforge.net/services/buy/index.php > > > _______________________________________________ > > > The BASE general discussion mailing list > > > basedb-users@lists.sourceforge.net > > > unsubscribe: send a mail with subject "unsubscribe" to > > > [EMAIL PROTECTED] > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
