Case study: Manual statistical testing with PROMPT
Keywords:
MannWhitney, Kolmogorov Smirnov, Fisher's exact test, ChiqSquare test, scripting, Java API, direct call
Questions:
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 (GO category) Category 2 (GO category) Total Class 1 (DE) n_{11} n_{12} n_{1+} Class 2 (not DE) n_{21} n_{22} n_{2+} Total n_{+1} n_{+2} n
Solutions:
There are multiple ways to perform statistical test manually with PROMPT:
A. Interactively in the PROMPT GUI
.
More:
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