Question: Modeling Microarray Chip Analysis In Gmod Chado
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gravatar for brianrepko
7.3 years ago by
brianrepko10
brianrepko10 wrote:

We are modeling Affymetrix (and other) CDFs, probesets, probes and alignments in Chado. We are doing this by making use of some of the mage module tables (ARRAYDESIGN, ELEMENT, ELEMENT_RELATIONSHIP) in addition to the main sequence module tables.

Our alignments are your basic match / match_part type features (we are doing 100% so we don't make them analysis features).

However, based on the alignments we do some calculations for probeset / gene attributes - specificity and sensitivity. These are calculated (R scripts) based on the alignments of the probes and the probeset to probe mapping in the CDF.

So now I have these scores for gene / probeset tuples and I'm not sure how to store those.

One thought is to model them as analysisfeatures with feature-relationships to the gene and probeset features. This would match how alignments are - analysisfeatures (match) with feature-locations to the features that are matched. But would use feature-relationships rather than feature-locations since its not a location thing.

The other thought is to make a feature-relationship between the gene and probeset features with a feature-relationship property of the sensitivity score and another feature-relationship property for the specificity score. This is easy to do but only works for properties that determined by 2 features. If I ever had an analysis that was determined by 3 variables, I couldn't do this.

Basically I have two functions from feature-x-feature --> [0,1] and need to store the data for various tuples.

Any thoughts as to the "Chado way" of modeling these types of analysis results?

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