Re: [basedb-devel] Have Raw Bioassay, want raw data file, fileformat and channels.

[Bob M. <r.m...@im...>]

Nicklas Nordborg writes:
 > 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 

So even though the two samples/biosources each have an annotation (one "male"
one "female"), you would recommend that the raw bioassay should inherit only
from one.

As discussed here:
http://www.mail-archive.com/bas...@li.../msg00907.html
inheriting from more than one item leads to undefined behaviour.

I'd like to suggest that one should be able to inherit annotations from
multiple biosources in a defined order (e.g. ch1, ch2).

Alternatively, some innate ordering of the labelled extracts with respect to
hyb (again in channel order).

 > 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.

Yes I agree that the BASE1 approach (different import configs for dye-swapped
hybs) is the way to avoid ratio mixups/complications during analysis.

cheers,
Bob


-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email r.m...@im...