## ----echo=FALSE, results="hide", warning=FALSE-------------------------------- suppressPackageStartupMessages({ library('arrays') }) ## ----echo=FALSE--------------------------------------------------------------- suppressPackageStartupMessages(library(limma)) suppressPackageStartupMessages(library(affy)) ## ----------------------------------------------------------------------------- ## Load packages library(affy) # Affymetrix pre-processing library(limma) # two-color pre-processing; differential # expression ## import "phenotype" data, describing the experimental design phenoData <- read.AnnotatedDataFrame(system.file("extdata", "pdata.txt", package="arrays")) ## RMA normalization celfiles <- system.file("extdata", package="arrays") eset <- justRMA(phenoData=phenoData, celfile.path=celfiles) ## differential expression combn <- factor(paste(pData(phenoData)[,1], pData(phenoData)[,2], sep = "_")) design <- model.matrix(~combn) # describe model to be fit fit <- lmFit(eset, design) # fit each probeset to model efit <- eBayes(fit) # empirical Bayes adjustment topTable(efit, coef=2) # table of differentially expressed probesets ## ----eval=FALSE--------------------------------------------------------------- # if (!"BiocManager" %in% rownames(installed.packages())) # install.packages("BiocManager") # BiocManager::install(c("affy", "limma"), dependencies=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("hgu95av2.db", dependencies=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # library("affy") # library("limma") ## ----eval=FALSE--------------------------------------------------------------- # browseVignettes(package="limma") ## ----eval=FALSE--------------------------------------------------------------- # help.start() ## ----------------------------------------------------------------------------- sessionInfo()