vegard nygaard wrote:
> Hi I am testing out the Illumina importer and have some questions.
>
> Can I connect the created raw bioassays to hybridizations (and indirectly to
> samples)?
Yes. When you run the importer you have the option to select a scan that
will be associated with the raw bioassays. The scan can be associated
with a hybridization which is then associated with labeled extracts, and
so on, up to samples.
> On the scan page I looked for a "associate raw bioassay" , but
> only found the "new raw bioassay".
You can select which scan a raw bioassay belongs to from the "Edit
rawbioassay" page.
> In order for the importer to be really
> useful I need to connect the raw data to samples in some way. From reading
> earlier posts it seems that connecting all the raw bioassays to one single
> scan is possible, but will there in upcoming base versions be more flexible
> association possibilities?
We have discussed this and came to the conclusion that the current
implementation is the most accurate representation of the process. The
BASE model assumes that there is a one-to-one relation between a slide
and hybridization. An Illumina slide has several (8 or more) arrays on a
single slide. This doesn't fit the current model in all aspects. Some
compromises has to be made. This is how we decided to do:
* The slide is represented a single ArraySlide item in the database
* The hybridization event links 8 (or more) labeled extracts to
the slide (one for each array)
* A single scan event represents the scanning
* One raw bioassay for each array is created
This will make is possible to accurately record scan and hybridization
parameters without having to duplicate (8 times) the same data. The
drawback is that the experiment validation will complain about the 8
labeled extracts since it expects only 1 for 1-channel data. It will
also complain about all labeled extracts having the same label. But
these warnings can be turned off. Another drawback is that all 8 labeled
extracts will be treated as parents to all 8 raw bioassays, even though
there really is a one-to-one relationship between those.
/Nicklas
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