Type of Tool  RFunction 
Title  Variance Smoothing of Fully Moderated tstatistic 
Programmer/Email  Lianbo Yu 
Contributing Site  other 
Description  This function computes posterior residual variances to be used in the denominator of a moderated tstatistic from a linear model analysis of microarray data. It is an extension of the moderated tstatistic 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 tstatistic is simply the sum of prior and residual variance degrees of freedom. 
Example  Example code 
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References  Yu L, Gulati P, Fernandez S, Pennell M, Kirschner L, Jarjoura D. Fully moderated tstatistic for small sample size gene expression arrays. Statistical Applications in Genetics and Molecular Biology, 2011; 10:article 42. 
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Software Program  R 
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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. 
RCode  Attachment  fmt.R 
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CreationDate  March, 2012 
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Notes1Legend  Section with calls to needed macros 
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Notes2Legend  Macro call with fully specified parameters 
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Notes3Legend  Section with definitions of global macro parameters 
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Notes4Legend  Section with definitions of local macro variables 
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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 

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manage  5 K  11 Dec 2012  20:35  UnknownUser 