## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), error=FALSE) ## ----load-data------------------------------------------------------------------------------------ library("airway") data(airway) ## ----play----------------------------------------------------------------------------------------- library("airway") data(airway) se <- airway se ## ----revise-se------------------------------------------------------------------------------------ head(assay(se)) colSums(assay(se)) colData(se) rowRanges(se) ## ----make-dds------------------------------------------------------------------------------------- library(DESeq2) dds <- DESeqDataSet(se, design = ~ cell + dex) ## ----do-rlog-------------------------------------------------------------------------------------- rld <- rlog(dds) head(assay(rld)) ## ----dist----------------------------------------------------------------------------------------- sampleDists <- dist( t( assay(rld) ) ) sampleDists ## ----message=FALSE-------------------------------------------------------------------------------- library("gplots") library("RColorBrewer") sampleDistMatrix <- as.matrix( sampleDists ) rownames(sampleDistMatrix) <- paste( rld$dex, rld$cell, sep="-" ) colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255) hc <- hclust(sampleDists) heatmap.2( sampleDistMatrix, Rowv=as.dendrogram(hc), symm=TRUE, trace="none", col=colors, margins=c(2,10), labCol=FALSE ) ## ----pca------------------------------------------------------------------------------------------ plotPCA(rld, intgroup = c("dex", "cell")) ## ----mds------------------------------------------------------------------------------------------ library(ggplot2) mds <- data.frame(cmdscale(sampleDistMatrix)) mds <- cbind(mds, colData(rld)) qplot(X1,X2,color=dex,shape=cell,data=as.data.frame(mds)) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()