Bob MacCallum wrote: > > We have solved this by making two different import configurations. > > This ensures that the sample is always in ch1 and the reference is in > > ch2 and there is no need to make a special formula to calculate the > > ratio. The information about dye-swapped or not is still interesting > > in the downstream analysis steps. In base1 I solved this by > > "annotating" the bioassays. I just added a prefix (_cy3 or _cy5) to > > the name. In base2 I would solve this by using the annotation system > > and annotate the RawBioAssay dye-swap true or false. To make the > > annotating a little easier we have added a ticket > (http://base.thep.lu.se/ticket/828 > > ) that will enable the user to automatically annotate the RawBioAssay > > depending on what configuration used to import the data. > > This looks good, but the question of whether a ch1/ch2 ratio is male/female or > female/male still remains open however. I can't see an easy way to slot a > "channel" attribute into the schema (probably for BioMaterialEvent, but this > wouldn't be relevant for the majority of events...).
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 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. /Nicklas ------------------------------------------------------------------------- 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
