Description Usage Arguments Details Value Author(s) See Also Examples

Write a microarray linear model fit to a file.

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`fit` |
object of class |

`results` |
object of class |

`file` |
character string giving path name for the output file. |

`digits` |
integer indicating rounding precision for output values. If |

`adjust` |
character string specifying multiple-testing adjustment method for the t-statistic P-values, e.g., |

`method` |
character string, should the P-value adjustment be |

`F.adjust` |
character string specifying adjustment method for the F-statistic P-values. |

`quote` |
logical value. If |

`sep` |
the field separator string. Values in the output file will be separated by this string. |

`row.names` |
logical value, whether to include row names in the output file. |

`...` |
other arguments are passed to |

This function writes a delimited text file containing for each gene (1) the average log2-intensity, (2) the coefficients or contrasts (log2-fold-changes), (3) moderated t-statistics, (4) t-statistic P-values, (5) F-statistic if available, (6) F-statistic P-values if available, (7) decideTests results if available and (8) gene names and annotation.

The `results`

argument is optional. If supplied, it should be the output from `decideTests`

for the same fit object, which indicates whether each contrast for each gene is considered statistically significant or not (coded 1 or -1 for positive or negative significant differences and 0 for non-significant values).

If `fit`

contains row names and `row.names=TRUE`

, then the row names will be the first column of the output file with a blank column heading.
This behaviour is analogous to that of `write.csv`

or to `write.table`

with `col.names=NA`

.

No value is produced but a file is written to the current working directory.

Gordon Smyth

`write.table`

or `write.csv`

in the base library.

An overview of linear model functions in limma is given by 06.LinearModels.

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