Case study: Manual statistical testing with PROMPT


Mann-Whitney, Kolmogorov Smirnov, Fisher's exact test, Chiq-Square test, scripting, Java API, direct call


1) Are two numeric sets differentially distributed?

Examples are in perparation

2) Is one or more categories over- or underrepresented?

Let's assume a typical statistical question in a microarray experiment as discussed in Rivals et al.(2007):
We consider a total population of genes, e.g. the genes expressed in a microarray experiment, and we are interested in the property of a gene to belong to a specific GO category. The aim is to establish whether the class of the differentially expressed (DE) genes presents an enrichment and/or a depletion of the GO category of interest with respect to the total gene population.

Let H0 denote the null hypothesis that the property for a gene to belong to the GO category of interest and that to be DE are independent, or equivalently that the DE genes are picked at random from the total gene population. This leads to a 2 x 2 contingency table.

Contingency Table Classification of the genes expressed in a microarray experiment

Category 1 (isinGO category) Category 2 ({notin}GO category) Total

Class 1 (DE) n11 n12 n1+
Class 2 (not DE) n21 n22 n2+
Total n+1 n+2 n



There are multiple ways to perform statistical test manually with PROMPT:

A. Interactively in the PROMPT GUI

B. Using the PROMPT Beanshell scripting method

C. Via the PROMPT Java API directly



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