## ----config, include=FALSE---------------------------------------------------- library(knitr) opts_chunk$set(dev = "jpeg", fig.height = 7.25, dpi = 72, fig.retina = 1) ## ----setup, warning=FALSE, message=FALSE, results="hide"---------------------- library(mimager) library(affydata) data("Dilution") ## ----default-image-n1, warning=FALSE, message=FALSE, fig.small=TRUE, fig.height=4---- mimage(Dilution, select = 1) ## ----default-image-n4--------------------------------------------------------- mimage(Dilution) ## ----default-image-1row, fig.wide=TRUE, fig.height=2.5------------------------ mimage(Dilution, select = c("10A", "20A", "10B", "20B"), nrow = 1) ## ----dilution-plm, message=FALSE---------------------------------------------- library(affyPLM) DilutionPLM <- fitPLM(Dilution) mimage(DilutionPLM) ## ----affyplm-signed-residuals------------------------------------------------- # use a divergent color palette for RLEs div.colors <- scales::brewer_pal(palette = "RdBu")(9) mimage(Dilution, transform = arle, legend.label = "RLE", colors = div.colors) ## ----dilution-array----------------------------------------------------------- DilutionArray <- marray(Dilution) dim(DilutionArray) ## ----dilution-arank----------------------------------------------------------- DilutionRank <- arank(DilutionArray) dim(DilutionRank)