## ----include=FALSE,cache=FALSE------------------------------------------------ library(codelink) library(knitr) opts_chunk$set(fig.align = 'center', concordance=TRUE,width=50,fig.show="hold", tidy = TRUE, comment = "", highlight = FALSE, prompt = TRUE) knit_hooks$set(no.mar = function(before, options, envir) { if (before) par(mar = rep(0,4)) # no margins. }) ## ----eval=FALSE--------------------------------------------------------------- # # NOT RUN # # library(codelink) # # to read data as CodelinkSet object: # f = list.files(pattern="TXT") # codset = readCodelinkSet(filename=f) # # NOT RUN # ## ----eval=FALSE--------------------------------------------------------------- # # NOT RUN # # pdata=read.AnnotatedDataFrame("targets.txt") # codset=readCodelinkSet(filename=pdata$FileName, phenoData=pdata) # # NOT RUN # ## ----------------------------------------------------------------------------- # sample dataset. data(codset) codset ## ----------------------------------------------------------------------------- data(codelink.example) print(is(codelink.example)) tmp=Codelink2CodelinkSet(codelink.example) tmp ## ----------------------------------------------------------------------------- w = createWeights(codset) ## NOTE: a proper replacement function will be provided later: assayDataElement(codset,"weight")=w ## ----------------------------------------------------------------------------- # get signal intensities. alias: getInt() head(exprs(codset)) # get background intensities. head(getBkg(codset)) # get SNR values. head(getSNR(codset)) # get flags. head(getFlag(codset)) # get weights. head(getWeight(codset)) # get phenoData: head(pData(codset)) ## ----------------------------------------------------------------------------- codset = codCorrect(codset, method = "half", offset = 0) ## ----------------------------------------------------------------------------- codset = codNormalize(codset, method = "quantile") ## ----eval=FALSE--------------------------------------------------------------- # # NOT RUN # codset = codNormalize(codset, method = "loess", weights=getWeight(codset), loess.method="fast") # # NOT RUN ## ----fig.cap="MA plot (left) and density plot (right).",fig.height=4,fig.width=4,out.width='.49\\linewidth'---- codPlot(codset) # by default MA plot. codPlot(codset, what="density") ## ----fig.cap="Pseudo image plot of an array",fig.height=1,fig.width=3--------- codPlot(codset, what="image") ## ----------------------------------------------------------------------------- fit = lmFit(codset, design=c(1,1,2,2), weights=getWeight(codset)) fit2 = eBayes(fit) topTable(fit2) ## ----------------------------------------------------------------------------- citation(package="codelink") ## ----------------------------------------------------------------------------- sessionInfo()