## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(DESeq2) library(limma) }) ## ----configure-test------------------------------------------------------------------------------- stopifnot( getRversion() >= '3.2' && getRversion() < '3.3', BiocInstaller::biocVersion() == "3.2" ) ## ----sleep-t.test--------------------------------------------------------------------------------- head(sleep) plot(extra ~ group, data = sleep) ## Traditional interface with(sleep, t.test(extra[group == 1], extra[group == 2])) ## Formula interface t.test(extra ~ group, sleep) ## equal variance between groups t.test(extra ~ group, sleep, var.equal=TRUE) ## ----sleep-lm------------------------------------------------------------------------------------- ## linear model; compare to t.test(var.equal=TRUE) fit <- lm(extra ~ group, sleep) anova(fit) ## ----sleep-model.matrix--------------------------------------------------------------------------- ## underlying model, used in `lm.fit()` model.matrix(extra ~ group, sleep) # last column indicates group effect model.matrix(extra ~ 0 + group, sleep) # contrast between columns ## ----sleep-diff----------------------------------------------------------------------------------- fit0 <- lm(extra ~ ID, sleep) fit1 <- lm(extra ~ ID + group, sleep) anova(fit0, fit1) t.test(extra ~ group, sleep, var.equal=TRUE, paired=TRUE)