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Qualitative-Concentration

Description

The “quantitative-concentration” module takes phenotype/bioactivity data, with the minimum inhibitory concentration per sample specified (concentration/dilution at which a phenotypic signal was still observed). Samples inactive at any concentration are specified with zero. The algorithm works as follows:

  • Duplicate measurements per sample are summarized with a user-specified algorithm (mean or median).
  • For each feature occurring in more than two active samples, the area per sample and the concentration measurement per sample are extracted.
  • The concentration are converted to their reciprocals (1 / measurement) or left at zero if the concentration was zero.
  • Both areas and reciprocals of concentration are z-transformed.
  • The transformed areas and percentages are correlated using the Pearson correlation.
  • The resulting p-value is corrected for multiple hypothesis testing using the Bonferroni-method (p-value * number of tested features).
  • If both correlation coefficient and p-value meet a user-specified cutoff, the phenotype information is assigned and the tested feature is considered bioactivity-associated.

Parameters

  • sample_avg: specifies the algorithm to summarize multiple measurements per sample for same assay. Possible algorithms are mean and median.
  • value: specifies value per feature to be correlated with concentration. Only area is currently allowed.
  • algorithm: specifies the statistical algorithm to use. Only pearson is currently allowed.
  • p_val_cutoff: Maximum Bonferroni-corrected p-value to consider, with zero disabling cutoff filtering for both p-value and coefficient.
  • coeff_cutoff: Minimum correlation coefficient to consider, with zero disabling cutoff filtering for both p-value and coefficient.

Limitations

  • This method assumes that the prerequisites with regard to sample reproducibility are met (see Input/Output).
  • This method assumes a negative linear relationship between phenotype (concentration) and concentration (area of feature) - the lower the minimal inhibitory concentration, the higher the concentration.
  • This method does not take into account any synergistic or quenching effects