IsoGenemSAM
The five SAM test statistics calculated for both the increasing and decreasing trends
The function calculates the values for the five SAM test statistics (the global likelihood test, Williams, Marcus, M, and the modified M) for the most likely direction.
 Keywords
 htest
Usage
IsoGenemSAM(x, y, fudge.factor)
Arguments
 x
 indicates the dose levels
 y
 gene expression for all genes
 fudge.factor
 the fudge factor values to be used in the SAM test statistics
Value

A list with components
 E2
 the SAM test statistic of global likelihood test for the likely direction of each gene.
 Williams
 the test statistic of Williams for the likely direction of each gene.
 Marcus
 the test statistic of Marcus for the likely direction of each gene.
 M
 the M test statistic for the likely direction of each gene.
 ModM
 the test statistic of the modified M for the likely direction of each gene.
 direction
 the direction with the higher likelihood of increasing (indicated by "u") or decreasing (indicated by "d") trend.
Note
This function calculates the five test statistics for both increasing and decreasing ordered alternatives for all the genes (rows in the data set).
References
Modeling Doseresponse Microarray Data in Early Drug Development Experiments Using R, Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors), (2012), Springer.
Testing for Trend in DoseResponse Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and ResamplingBased Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.
IsoGene: An R Package for Analyzing Doseresponse Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2/1.