Nicklas Nordborg wrote: > tr...@valdelsa.net wrote: > >> Hi, I'd like to suggest to MEV Launcher developers to implement 2-3 >> fundamental functionalities: >> >> 1. Log2 ratio transform >> > > This was how data was originally exported by BASE, but it turned out > that MeV could not handle that (except for one-channel data). But MeV > has been upgraded since then so maybe it is possible now. It needs to be > investigated. For background info see: http://base.thep.lu.se/ticket/942 > > Maybe I'm wrong, but MEV always supposes to have log2 transformed data (since the first release). Instead, if you import experiments with one color or two color separated channels, then MEV supposes to have non log2 transformed data. There's another situation in which some old version of MEV supposes to have non log transformed data: if it doesn't find (in a non specified number of initial lines!?) any negative value then it switches to direct ratios (non log2 transformed data)
>> 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. >> 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. >> These three missing options, I think, at the moment are limiting a >> lot the usability of the plugin, still forcing the users to export >> data with the classical BASEexporter (and then manipulating them, in >> some way, because they don't fit MEV requirements). >> >> This would be very helpful >> > > Thanks for the suggestions. By the way... patches are always welcome. > Yes, I know the huge effort that you are doing on the BASE2 project, I appreciate it very much. My point was to have again similar functionalities (at least 1 and 2) that were present in BASE1... 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. Thankyou, bye, Ax > /Nicklas > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > 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 > > ------------------------------------------------------------------------------ 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
