This function produces several figures to examine quality scores.

1 2 3 |

`object1` |
a list containing two elements: ct (the expression estiamtes) and qc (quality scores) |

`object2` |
an optional second list of the same format as object1, used to compare two methods. |

`cloglog1` |
if TRUE, the -log(-log(object1$qc)) is plotted. This is useful to visualize certain quality scores such as R-squared. |

`cloglog2` |
if TRUE, the -log(-log(object2$qc)) is plotted. This is useful to visualize certain quality scores such as R-squared. |

`na.rm` |
if TRUE, quality scores corresponding to NA expression estimates are removed from analysis. This is only used if plotType=="boxplot". |

`plotType` |
type of plot to return. Options are a scatterplot or a boxplot. |

`label1` |
optional label corresponding to object 1 to be used in plotting. |

`label2` |
optional label corresponding to object 2 to be used in plotting. |

The function generates a plot of the desired type.

Matthew N. McCall

1 2 3 4 5 | ```
data(lifetech)
qualityAssessment(lifetech, plotType="boxplot")
data(qpcRdefault)
qualityAssessment(object1=lifetech,object2=qpcRdefault,cloglog2=TRUE)
``` |

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