### R code from vignette source 'metaArray.Rnw' ################################################### ### code chunk number 1: metaArray.Rnw:44-70 ################################################### library(metaArray) library(Biobase) library(MergeMaid) data(mdata) common <- intersect(rownames(chen.poe),rownames(garber.poe)) common <- intersect(common, rownames(lapointe.poe)) chen.poe <- chen.poe[match(common, rownames(chen.poe)),] garber.poe <- garber.poe[match(common, rownames(garber.poe)),] lapointe.poe <- lapointe.poe[match(common, rownames(lapointe.poe)),] vars <- list("var1","var2") names(vars) <- names(chen.spl) pdata1 <- new("AnnotatedDataFrame") pData(pdata1) <- chen.spl varLabels(pdata1) <- vars sample1 <- new("ExpressionSet", exprs=chen.poe, phenoData = pdata1) names(vars) <- names(garber.spl) pdata2 <- new("AnnotatedDataFrame") pData(pdata2) <- garber.spl varLabels(pdata2) <- vars sample2 <- new("ExpressionSet", exprs=garber.poe, phenoData = pdata2) names(vars) <- names(lapointe.spl) pdata3 <- new("AnnotatedDataFrame") pData(pdata3) <- lapointe.spl varLabels(pdata3) <- vars sample3 <- new("ExpressionSet", exprs=lapointe.poe, phenoData = pdata3) merged <- mergeExprs(sample1,sample2,sample3) ################################################### ### code chunk number 2: metaArray.Rnw:82-88 (eval = FALSE) ################################################### ## merged.cor <- intcor(merged)$avg.cor ## mData <- exprs(intersection(merged)); mCl <- NULL ## mData <- mData[merged.cor > median(merged.cor),] ## for(i in 1:length(merged)) { ## mCl <- c(mCl, pData(merged[i])$metastasis) ## } ################################################### ### code chunk number 3: metaArray.Rnw:103-104 ################################################### em.draw(as.numeric(chen[1,]), cl=ncol(chen)) ################################################### ### code chunk number 4: metaArray.Rnw:111-112 (eval = FALSE) ################################################### ## z.stat <- Zscore(merged)