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Question: sizepower
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5.6 years ago by
Michael Salbaum80 wrote:
Dear All, I wonder if someone could point me towards some guidance using the package 'sizepower'. The archives have not netted much in this regard; the vignette was very useful. I'm doing a prospective power analysis for an array experiment with a matched pair design. I found the function power.matched(ERO, G0, absMu1, sigmaD, n) useful, however, I have a few questions. Two issues: 1. I don't have a good feel for the parameter ER0 - mean number of false positives. Of course I'd like it to be as low as possible, so I simply ran scenarios with setting ER0 at numbers we'd be able to tolerate and calculate power/sample size accordingly. 2. Pardon my ignorance, but I'm also struggling with parameter G0 - anticipated number of genes in the experiment that are not differentially expressed. At the moment, I'm assuming G0=G i.e. number of gene (probes) tested. Does G0 need to be based on the number of gene probes on the array (~46,000)? Inspecting a similar paradigm on the same array platform on GEO reveals that only about ~12,000 gene probes are consistently detected. I'm aware that it doesn't make a huge difference (and almost none in practical terms), but I'm curious. I've left the parameter absMu1 at 1 (as I understand it, this represents effect size, as fold change of at least 2). My sigmaD parameter comes from a preliminary experiment: gene expression by qPCR, standard deviation of the (log2) differences between pairs. Thanks for the help. Cheers, michael P.S. If I should be using a different package for the task at hand, I'd like to hear such a recommendation as well - thanks. R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.52 (6188) x86_64-apple-darwin9.8.0] [Workspace restored from /Users/jms/.RData] [History restored from /Users/jms/.Rapp.history] > library(sizepower) > power.matched(1, 12000, 1, 0.731, 20) $power [1] 0.9854905$psi1 [1] 37.42788 > power.matched(1, 46000, 1, 0.731, 20) $power [1] 0.9693688$psi1 [1] 37.42788 > J. Michael Salbaum, Ph.D. Associate Professor Pennington Biomedical Research Center Louisiana State University System 6400 Perkins Road Baton Rouge, LA 70808 (225) 763-2782 [[alternative HTML version deleted]]