## ----setup, echo=FALSE--------------------------------------------------- library(LearnBioconductor) stopifnot(BiocInstaller::biocVersion() == "3.1") ## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ----ggplot-setup, eval=FALSE-------------------------------------------- # library(DESeq2) # library(airway) # data(airway) # se = airway # dds <- DESeqDataSet(se, design = ~ cell + dex) # dds$dex <- relevel(dds$dex, "untrt") # dds <- DESeq(dds) # res <- results(dds) # resdf <- as.data.frame(res) ## ----volcano, eval=FALSE------------------------------------------------- # plot(-log10(padj) ~ log2FoldChange, resdf)