# IsoGenemSAM

0th

Percentile

##### 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 Dose-response 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 Dose-Response Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and Resampling-Based Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.

IsoGene: An R Package for Analyzing Dose-response 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.

isoreg, IsoGene1, Isofudge