Description Usage Arguments Value Note Author(s) References See Also Examples

This is a modified version of the R script "ComBat.R" (see references). It is used to adjust for batch effects in microarray data. The modification is restricted to make the script accept expression matrices and data.frames instead of plain text files.

1 |

`expression_xls` |
The expression matrix to adjust. |

`sample_info_file` |
The sample information data.frame regarding batch contribution and possibly covariates. |

`type` |
The type of input; Defaults to "txt". |

`write` |
Write output to external file or provide new expression matrix. |

`covariates` |
Describe which Covariates to use in the process and which to dismiss. The default is to use only "Batch". |

`par.prior` |
Logical; set prior parameters or not; Use prespecified values for the variables ("TRUE") or start a priori ("FALSE"). |

`filter` |
Filter for genes not present in a given percentage of the samples. Requires present/absent calls in the data. Can be either "FALSE" or a numeric between "0" and "1". Recommended is "0.8" or "FALSE". |

`skip` |
Columns to skip in the input "expression_xls" matrix. |

`prior.plots` |
Create quantile-quantile and kernel density plots including prior estimates to assess the quality of the estimation. |

Returns a matrix holding adjusted expression values.

Original code by Johnson, WE, Rabinovic, A, and Li, C, made available in this package by Andreas Heider

Original author: Johnson, WE, Rabinovic, A, and Li, C (2007)

Modified by: Andreas Heider (2011)

Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.

virtualArray-package, virtualArray.ExpressionSet, virtualArrayCompile

1 | ```
## EMPTY
``` |

virtualArray documentation built on Sept. 12, 2016, 6:10 a.m.

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