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Unformatted text preview: 1 1 Introduction to Limma Package in R Peng Liu 4/8/2008 2 Limma Package in R Â¡ It is developed by Gordon Smyth and information about is can be found at: http://bioinf.wehi.edu.au/limma/ Â¡ Download limma package source("http://www.bioconductor.org/biocLite.R") biocLite("limma") Â¡ You can find the location of the pdf file of userâ€™s guide for limma and open it using: library(limma) limmaUsersGuide() 3 Example Â¡ We will use one data set example in the paper of moderated t-test: Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3 , No. 1, Article 3. Â¡ The data is referred to in the paper as ApoAI data and can be downloaded from http://bioinf.wehi.edu.au/limmaGUI/DataSets.html 4 Experimental Design Â¡ Two treatment groups: ApoAI knockout and normal mice....
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- Spring '08
- Statistics, limma, limma package, Gordon Smyth