Description Usage Arguments Details Value Author(s) Examples

`RLEPlot`

generates three different types of relative log expression plots for high-dimensional data.

1 2 3 |

`X` |
A matrix of gene expression values. |

`Y` |
A matrix of gene expression values. |

`center` |
A logical scalar; |

`name` |
A vector of characters describing the data contained in |

`title` |
A character string describing the title of the plot. |

`method` |
The type of RLE plot to be displayed; possible inputs are |

`anno` |
A dataframe or a matrix containing the annotation of arrays in |

`Factor` |
A character string corresponding to a column name of |

`numeric` |
A logical scalar indicating whether |

`new.legend` |
A vector describing the names used for labelling; if |

`outlier` |
A logical indicating whether outliers should be plotted; only applicable when |

There are three different RLE plots that can be generated using `RLEPlot`

:

`"IQR.points"`

Median expression vs. inter-quantile range of every array.

`"IQR.boxplots"`

Boxplots of the 25% and 75% quantile of all arrays.

`"Minmax"`

Ordinary RLE plots for the 5 arrays with the smallest and largest inter-quantile ranges.

Note that normal RLE plots are not supplied as they are not very suitable for high-dimensional data.

`RLEPlot`

returns a plot.

Saskia Freytag

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 250, 100, check.input=FALSE)
Y.hat<-RUVNaiveRidge(Y, center=TRUE, nc_index=251:500, 0, 10, check.input=TRUE)
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.points")
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.boxplots")
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="minmax")
#Create a random annotation file
anno<-as.matrix(sample(1:4, dim(Y.hat)[1], replace=TRUE))
colnames(anno)<-"Factor"
try(dev.off(), silent=TRUE)
RLEPlot(Y$Y, Y.hat, name=c("Raw", "RUV"), title="", method="IQR.points",
anno=anno, Factor="Factor", numeric=TRUE)
``` |

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