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fmt.R: fmt

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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	fmt.R
R-Code
SAS-Code - Attachment
SAS-Code
Stata-Code - Attachment
Stata-Code
Other Code - Attachment
Other Code
Called Data Manipulation
Called Tool/Utility
Called Checking Macro
Called Other
Creation-Date	March, 2012
Revision-Date
Example Code
Example Output
SAS Examples
SAS_Example_Code
SAS_Example_Output
R Examples
R_Example_Code
R_Example_Output
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.
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I	Attachment	Action	Size	Date	Who	Comment
R	fmt.R	manage	5 K	11 Dec 2012 - 20:35	UnknownUser

This topic: CTSpedia > WebHome > StatToolsHome > StatToolsTopic065
Topic revision: 11 Dec 2012, LianboYu

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