Likelihood Ratio Test Statistic (E2)

There are three methods for computing E2 in the ISOGeneGUI. First is asymptotic, second is using permutations and last is using faster implementation of permutation testing from package orQA.

1. Asymptotic method
This options provides the analysis using the E2 test statistics based on p-values obtained from its exact distribution. The provided p-values adjustment methods are BH, BY, Holm, SidakSS, Sidak SD, Holm, Hochberg and Bonferroni. Based on the specified adjustment methods and overall significant level, the list of significant genes along isotonic means difference, test statistic value, raw and adjusted p-values, will be produced.
Analysis > Likelihood Ratio Test (E2): Asymptotic
Screenshot of the main dialog box of Likelihood Ratio Test (E2) analysis: Asymptotic

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Screenshot of the list of significant genes
Plots
After the raw p-values and adjusted p-values are calculated, there are three plot that can be produced. After choose the option and click the Produce plots button the plot will be displayed.
Screenshot of the plot of Fold change vs. E2
2. Permutation (IsoGene)
This options is described in Permutation method.
3. Permutation (orQA)
Last option is using implementation from package orQA. The function e2test is used. The function is originally aimed for resampling within one mouse (in the context of experiment described in orQA package). However, we are using the method in the way that resampling is done across all observation, i.e. considering all our observations independent.
Screenshot of the main dialog box of Likelihood Ratio Test (E2) analysis: orQA
Plots
After the raw p-values and adjusted p-values are calculated, there are two plot that can be produced. After choose the option and click the Produce plots button the plot will be displayed.
Screenshot of the plot of the p-values
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