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.

1 | ```
IsoGenemSAM(x, y, fudge.factor)
``` |

`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 |

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. |

This function calculates the five test statistics for both increasing and decreasing ordered alternatives for all the genes (rows in the data set).

Lin et al.

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`

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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