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

ADD COMMENTlink written 7.3 years ago by brianrepko10
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