## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## pre-load to avoid load messages in report library(Glimma) library(limma) library(edgeR) ## ----------------------------------------------------------------------------- library(Glimma) library(limma) library(edgeR) dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma")) ## ----------------------------------------------------------------------------- glimmaMDS(dge) ## ----------------------------------------------------------------------------- design <- readRDS( system.file("RNAseq123/design.rds", package = "Glimma")) contr.matrix <- readRDS( system.file("RNAseq123/contr.matrix.rds", package = "Glimma")) ## ----------------------------------------------------------------------------- v <- voom(dge, design) vfit <- lmFit(v, design) vfit <- contrasts.fit(vfit, contrasts = contr.matrix) efit <- eBayes(vfit) ## ----------------------------------------------------------------------------- dge <- estimateDisp(dge, design) gfit <- glmFit(dge, design) glrt <- glmLRT(gfit, design, contrast = contr.matrix) ## ----------------------------------------------------------------------------- glimmaMA(efit, dge = dge) # glimmaMA(glrt, dge = dge) to use edgeR results ## ----------------------------------------------------------------------------- glimmaVolcano(efit, dge = dge) ## ---- eval = FALSE------------------------------------------------------------ # htmlwidgets::saveWidget(glimmaMA(efit, dge = dge), "ma-plot.html") # # you can link to it in Rmarkdown using [MA-plot](ma-plot.html) ## ----------------------------------------------------------------------------- sessionInfo()