Description Usage Arguments Details Value Author(s) References Examples

Estimate the calibration model parameters according to the known concentration and the measured intensities of external control spikes on each array.

1 | ```
estimateParameter(spike, RG, bc = FALSE, area = TRUE, errormodel = "M")
``` |

`spike` |
a |

`RG` |
a |

`bc` |
a logical value. |

`area` |
a logical value. |

`errormodel` |
a character to indicate the distribution of spot capacity. "A" means spot capacity is additive. "M" means spot capacity is multiplicative. Default is "M". |

This function estimates calibration model parameters. In this function,
the model parameters are estimated separately for each microarray,
based on the measured intensities of the external control spikes and
their known concentration in the hybridization solution. It accepts
spike measured intensities and concentration from `spike`

argument,
which is an object of `SpikeList`

class.

It supports different ways to calculate the measured intensities.
Arguments `bc`

and `area`

are logical and their combinations is used
for specifying four differents ways. `bc`

indicates using background correction
or not. `area`

indicates multiplying spot area or not. The default value
of these two arguments are `bc`

= FALSE and `area`

= TRUE.

The argument `errormodel`

is to specify the distribution of spot capacity
of each array. The spot capacity is either additive or multiplicative.
Whichever distribution is more appropriate will depend largely on the type of
microarray slide and spotting procedure used. The spot parameters mus and sigmas
can be considered equal for all measurements of a single array.

The argument `RG`

is for calculating the maximum intensity of each array. These
maximum intensities are used to estimate the upper saturation level of each array.

More details please refer to the reference literature.

An `ParameterList`

object containing the components:

`MuS` |
matrix containing MuS for each array. |

`Ka` |
matrix containing Ka for each array. |

`P1` |
matrix containing P1 of each dye for each array. |

`P2` |
matrix containing P2 of each dye for each array. |

`SigmaA` |
matrix containing sigma additive for each array. |

`SigmaM` |
matrix containing sigma multiplicative for each array. |

`SigmaS` |
matrix containing sigma spoterror for each array. |

`SpotError` |
matrix containing the spot error of each spot for each array. |

`Method` |
boolean values indicating the way to calculate the measured intensities. |

`ErrorModel` |
character |

Hui Zhao

Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22: 1251-1258.

1 2 3 4 5 6 7 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.