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This topic: CTSpedia > WebHome > StatToolsHome > StatToolsTopic065

Topic revision: 11 Dec 2012, LianboYu

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- fmt.R: fmt

Type of Tool | R-Function |

Title | Variance Smoothing of Fully Moderated t-statistic |

Programmer/Email | Lianbo Yu |

Contributing Site | other |

Description | This function computes posterior residual variances to be used in the denominator of a moderated t-statistic from a linear model analysis of microarray data. It is an extension of the moderated t-statistic original proposed by Smyth (2004). LOESS local regression and empirical Bayesian method are used to estimate gene specific prior degrees of freedom and prior variance based on average gene intensity level. The posterior residual variance in the denominator is a weighted average of prior and residual variance and the weights are prior degrees of freedom and residual variance degrees of freedom. The degrees of freedom of the moderated t-statistic is simply the sum of prior and residual variance degrees of freedom. |

Example | Example code |

Classification Graph Type | |

Graph_Type | |

References | Yu L, Gulati P, Fernandez S, Pennell M, Kirschner L, Jarjoura D. Fully moderated t-statistic for small sample size gene expression arrays. Statistical Applications in Genetics and Molecular Biology, 2011; 10:article 42. |

Datasets | |

Data | |

Software Program | R |

Software | |

Macro Parameters | Amean: vector of residual variances of all genes. df: degrees of freedom for sigmasq. span1: span parameter in LOESS smoothing function. span2: span parameter in LOESS smoothing function. iter1: iteration number in LOESS smoothing function. iter2: iteration number in LOESS smoothing function. b: number of genes on either side of moving average window when calculating variance of log residual variances. |

R-Code - Attachment | http://biostat1478.dhcp.mc.vanderbilt.edu/foswiki/pub/CTSpedia/StatToolsTopic065/fmt.R |

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SAS-Code | |

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Other Code | |

Called Data Manipulation | |

Called Tool/Utility | |

Called Checking Macro | |

Called Other | |

Creation-Date | March, 2012 |

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Example Code | |

Example Output | |

SAS Examples | |

SAS_Example_Code | |

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R Examples | |

R_Example_Code | |

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Stats Examples | |

Special Features | |

Special Features Attached | |

Special Features Text | |

Notes1-Legend | Section with calls to needed macros |

Notes1 | |

Notes2-Legend | Macro call with fully specified parameters |

Notes2 | |

Notes3-Legend | Section with definitions of global macro parameters |

Notes3 | |

Notes4-Legend | Section with definitions of local macro variables |

Notes4 | |

See Also | |

Checklists | |

Stat Tools Disclaimer | This tool is also available in R package fmt. |

Discliamer | The views expressed within CTSpedia are those of the author and must not be taken to represent policy or guidance on the behalf of any organization or institution with which the author is affiliated. |

Permission | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT OLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |

Reference Image |

I | Attachment | Action | Size | Date | Who | Comment |
---|---|---|---|---|---|---|

R | |
manage | 5 K | 11 Dec 2012 - 20:35 | UnknownUser |

Topic revision: 11 Dec 2012, LianboYu

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