# #——包括= FALSE,缓存= FALSE ------------------------------------------------ 库(codelink)库(knitr) opts_chunk美元设置(图。align = 'center'， concordance=TRUE,width=50，图。show="hold"， tidy = TRUE, comment =" "， highlight = FALSE, prompt = TRUE)Mar = function(before, options, envir) {if (before) par(Mar = rep(0,4)) #无边框。}) ## ---- eval = FALSE --------------------------------------------------------------- # # 不运行(codelink) # # # #库读取数据作为CodelinkSet对象:# f = list.files(模式=“三种”)# codset = readCodelinkSet(文件名= f) # #不会运行 # ## ---- eval = FALSE --------------------------------------------------------------- # # 没有运行# # pdata = read.AnnotatedDataFrame (targets.txt) # codset = readCodelinkSet(文件名= pdata $文件名,phenoData = pdata) # #不会运行 # ## ----------------------------------------------------------------------------- # 样本数据集。数据(codset) codset ## ----------------------------------------------------------------------------- 数据(codelink.example)打印((codelink.example)) tmp = Codelink2CodelinkSet codelink.example tmp ## ----------------------------------------------------------------------------- w = createWeights (codset) # #注:在本文的后面我们将会提供一个适当的替代函数:assayDataElement (codset“重量”)= w ## ----------------------------------------------------------------------------- # 得到的信号强度。alias: getInt() head(exprs(codset)) #获取背景强度。head(getBkg(codset)) #获取信噪比值。head(getSNR(codset)) # get标志。head(getFlag(codset)) #获取权重。 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()