> 15 nov 2007 kl. 21.32 Bob MacCallum wrote: > > > Vegard, did you come up with a work-around? Should one import all > > data "straight" and use the dyes as a proxy for the channel number?
No I did not. I planned to either convince my self that BASE2's model was sufficient or make a dye-swap example showing Lund that it was not. I was derailed by other work and did neither. > > Johan 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. When analyzing in BASE1 it was often the case that we suspected mix up of the channels in experiments involving dye swaps, like a mild paranoia. So I think it is important for the user to be able to check what import configuration and raw data file was used in making a raw data set. This might have been implemented for BASE2.5, but I have not had time to check out yet. Vegard. ------------------------------------------------------------------------- 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
