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Qualitative

Description

The “qualitative” module takes qualitative phenotype/bioactivity data. Samples are either considered “positive” or “negative”. The algorithm works as follows:

  • Features exclusively detected in the “positive” samples are considered phenotype/bioactivity-associated.
  • Features exclusively detected in the “negative” samples are considered NOT phenotype/bioactivity-associated.
  • For features detected in both “positive” and “negative” samples, a user-specified feature value (height or area) across “positive” and “negative” samples is compared using a user-specified algorithm. If the resulting quotient is greater than a user-specified ratio (fold-change), the feature is considered phenotype/bioactivity-associated; else, it is not. This allows to retain features that may be bioactivity-associated but are present in sub-inhibitory concentrations in the “negative” samples (lack of phenotypic/bioactivity readout). The fold-change is then registered as the phenotype score.

Parameters

  • factor: the user-specified ratio (fold change) to differentiate features detected in both “positive” and “negative” samples.
  • value: the value used in the determination of the quotient: either “height” or “area”.
  • algorithm: the algorithm to summarize values over “positive” and “negative” samples. Currently possible algorithms are “mean”, “median”, and “minmax”. The latter takes the lowest value across “positive” samples and the highest value across “negative” samples

Limitations

  • Contrary to Quantitative-Percentage and Quantitative-Concentration, this module does not perform predictions - it rather excludes features that are unlikely to be associated with the observed phenotype.
  • This method assumes that the prerequisites with regard to sample reproducibility are met (see Input/Output).