15 nov 2007 kl. 21.32 skrev Bob MacCallum:
> 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? If raw
> bioassays are annotated as "dye-swap" would one need to create a
> ratio formula
> that did something like this:
>
> if(rawbioassay.isAnnotated("dye swap", true), ch(2)/ch(1), ch(1)/
> ch(2))
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.
/Johan
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