## ----cwd,echo=FALSE,results='hide'-------------------------------------------- cwd <- getwd() ## ----pkgs, results = 'hide', message = FALSE, warning = FALSE----------------- library("affy") library("estrogen") library("vsn") library("genefilter") ## ----datadir------------------------------------------------------------------ system.file("extdata", package="estrogen") datadir <- function(x) file.path(system.file("extdata", package="estrogen"), x) ## ----loadpdata---------------------------------------------------------------- pd <- read.AnnotatedDataFrame(datadir("estrogen.txt"), header = TRUE, sep = "", row.names = 1) pData(pd) ## ----a.read,results='hide'---------------------------------------------------- a <- ReadAffy(filenames = datadir(rownames(pData(pd))), phenoData = pd, verbose = TRUE) ## ----a.show------------------------------------------------------------------- a ## ----x.calc, results='hide'--------------------------------------------------- x <- vsnrma(a) ## ----x.show------------------------------------------------------------------- x ## ----image1, dev = "png", include = FALSE------------------------------------- image(a[, 1]) ## ----image2, dev = "png", include = FALSE------------------------------------- badc <- ReadAffy(filenames = datadir("bad.cel")) image(badc) ## ----hist, include = FALSE, fig.width = 5, fig.height = 5--------------------- hist(log2(intensity(a[, 4])), breaks=100, col="blue") ## ----boxplots, include = FALSE, fig.width = 4, fig.height = 5----------------- boxplot(a,col="red") boxplot(data.frame(exprs(x)), col="blue") ## ----classx------------------------------------------------------------------- class(x) class(exprs(x)) ## ----scp, include = FALSE, results='hide', fig.width = 6, fig.height = 6, dev = "png", dpi = 180---- plot(exprs(a)[, 1:2], log="xy", pch=".", main="all") plot(pm(a)[, 1:2], log="xy", pch=".", main="pm") plot(mm(a)[, 1:2], log="xy", pch=".", main="mm") plot(exprs(x)[, 1:2], pch=".", main="x") ## ----heatmapa----------------------------------------------------------------- rsd <- rowSds(exprs(x)) sel <- order(rsd, decreasing=TRUE)[1:50] ## ----heatmap, include = FALSE, fig.width = 6, fig.height = 6, dev = "png", dpi = 180---- heatmap(exprs(x)[sel, ], col = gentlecol(256)) ## ----deflm-------------------------------------------------------------------- lm.coef <- function(y) lm(y ~ estrogen * time.h)$coefficients eff <- esApply(x, 1, lm.coef) ## ----showlmres---------------------------------------------------------------- dim(eff) rownames(eff) affyids <- colnames(eff) ## ----gn----------------------------------------------------------------------- library(hgu95av2.db) ls("package:hgu95av2.db") ## ----eff-show, fig.width = 5, fig.height = 4---------------------------------- hist(eff[2,], breaks=100, col="blue", main="estrogen main effect") lowest <- sort(eff[2,], decreasing=FALSE)[1:3] mget(names(lowest), hgu95av2GENENAME) highest <- sort(eff[2,], decreasing=TRUE)[1:3] mget(names(highest), hgu95av2GENENAME) hist(eff[4,], breaks=100, col="blue", main="estrogen:time interaction") highia <- sort(eff[4,], decreasing=TRUE)[1:3] mget(names(highia), hgu95av2GENENAME)