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Table 1 Parameters used for prediction analysis and their properties

From: Predicting gene ontology from a global meta-analysis of 1-color microarray experiments

Parameter Information it gives Drawback
Total = Frequency of gene pair co-expression Total number of times a gene pair is expressed, excluding missing values Some genes are expressed more frequently than others
MIM = Mutual Information Measure Specificity of co-expression When Total is small, MIM can be artificially high
R2 = Pearson’s Correlation Coefficient Correlation between gene pair expression levels Will detect global, but not conditional, co-regulation. Also, non-expression is far more common than expression, biasing R2 (e.g., 2 genes never expressed will show perfect correlation)
P = Purity When co-expression “behavior” is described in terms of discrete categories, purity reflects a relative breakdown of behavioral observations Information can be lost when discretizing a continuous variable