## ----init, echo=FALSE--------------------------- options(width=50) library(knitr) library(lattice) library(xtable) ## ----cache=TRUE--------------------------------- suppressPackageStartupMessages(library(methylumi,quietly=TRUE)) samps <- read.table(system.file("extdata/samples.txt", package = "methylumi"),sep="\t",header=TRUE) mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',package='methylumi'), qcfile=system.file('extdata/exampledata.controls.txt',package="methylumi"), sampleDescriptions=samps) ## ----cache=FALSE-------------------------------- mldat ## ----cache=TRUE--------------------------------- getAssayDataNameSubstitutions() ## ----cache=TRUE--------------------------------- md <- cmdscale(dist(t(exprs(mldat)[fData(mldat)$CHROMOSOME=='X',])),2) ## ----cache=FALSE-------------------------------- plot(md,pch=c('F','M')[pData(mldat)$Gender],col=c('red','blue')[pData(mldat)$Gender]) ## ----cache=FALSE-------------------------------- avgPval <- colMeans(pvals(mldat)) par(las=2) barplot(avgPval,ylab="Average P-Value") ## ----cache=FALSE-------------------------------- controlTypes(mldat) ## ----cache=FALSE-------------------------------- qcplot(mldat,"FIRST HYBRIDIZATION") ## ----cache=TRUE--------------------------------- toKeep <- (avgPval<0.05) pData(mldat)$Gender[9] <- "F" mldat.norm <- normalizeMethyLumiSet(mldat[,toKeep]) ## ----cache=TRUE--------------------------------- library(limma) dm <- model.matrix(~1+Gender,data=pData(mldat.norm)) colnames(dm) fit1 <- lmFit(exprs(mldat.norm),dm) fit2 <- eBayes(fit1) tt <- topTable(fit2,coef=2,genelist=fData(mldat.norm)[,c('SYMBOL','CHROMOSOME')],number=1536) x <- aggregate(tt$adj.P.Val,by=list(tt$CHROMOSOME),median) colnames(x) <- c('Chromosome','Median adjusted P-value') ## ----results='asis'----------------------------- library(xtable) xt <- xtable(x,label="tab:chromosomepvals",caption="The median adjusted p-value for each chromosome showing that the X-chromosome is highly significantly different between males and females") digits(xt) <- 6 print(xt,include.rownames=FALSE,align="cr") ## ----genderProbesByChrom,fig.keep='high'-------- print(xyplot(-log10(adj.P.Val)~CHROMOSOME, tt,ylab="-log10(Adjusted P-value)", main="P-values for probes\ndistinguising males from females")) ## ----results='asis'----------------------------- toLatex(sessionInfo())