# Test of monotonic trends using the five test statistics with BH or BY adjustment

### Description

The function adjusts for the raw p-values of the five test statistics using BH or BY procedure.

### Usage

1 2 |

### Arguments

`rp` |
raw p-value matrix with each row for one gene and 6 columns, the first column contains the Probe.ID, the second to the sixth columns are raw p-values for the five test statistics |

`FDR` |
the desired FDR to control |

`type` |
choose BH or BY procedure to control FDR |

`stat` |
choose one of the five test statistics to use |

### Details

The input raw p-values to this function can be the one sided or the two sided ones which are obtained using function raw.p. The results using one sided p-values and FDR controlling at alpha/2 is equivalent to that using two sided p-values and FDR controlling at alpha.

### Value

`sign.genes` |
A list of significant genes while controlling FDR is obtained, with 4 columns: the first column is the probe ID, the second column is the row id, the third column is the raw p-values of the significant genes and the last column is the adjusted p-values of significant genes using BH or BY procedure |

### Note

This function only allows one type of FDR adjustment, either BH or
BY. For other type of adjustment, see function `mt.rawp2adjp`

in package `multtest`

.

### Author(s)

Lin et al.

### References

package `multtest`

Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors). (2012) Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R. Springer.

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.

### See Also

'mt.rawp2adjp', `IsoRawp`

### Examples

1 2 3 |