Opened 14 years ago

Last modified 14 years ago

#868 closed enhancement

Support for chips with multiple arrays — at Version 1

Reported by: Nicklas Nordborg Owned by: everyone
Priority: major Milestone: BASE 2.6
Component: core Version:
Keywords: Cc:

Description (last modified by Nicklas Nordborg)

Illumina array slides are special in that they contain multiple "sections" on a single array chip. When hybridizing a slide each section is hybridized with a different sample. This can already be represented in the database by selecting multiple labeled extract and connecting them to the same hybridization. But, this is actually a "misuse" since the assumption is that all labeled extract are used on the entire slide and that they all should have different labels. Since Illumina is a one-channel platform, the experiment validator will complain about the number of labeled extracts not being 1, and that they don't have different labels. Another problem is that it is not possible to know which raw bioassay is related to what labeled extract. In the real world, there is a one-to-one relationship, but in BASE this is lost and it seems like all labeled extracts are associated with all raw bioassay. This will make it hard and confusing when using the experiment overview since all labeled extracts can be reached from all raw bioassays.

So, we need to add information about the number of sub arrays on a slide (possible already at the array design level). We need to be able to associate a specific labeled extract to a specific sub-array, and we also need to associate the related raw bioassay to the same sub-array.

If we could do this from scratch without having to worry about backwards compatibility it would probably be easy. I think the hard part is to maintain the backwards compatibility.

Change History (1)

comment:1 Changed 14 years ago by Nicklas Nordborg

Description: modified (diff)
Priority: majorcritical
Summary: Support for multiple (sub)hybridizations on the same array slideSupport for chips with multiple arrays
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