# #——风格,eval = TRUE,呼应= FALSE,结果= "飞机 "-------------------------- 美元knitr: opts_chunk集(消息= FALSE,警告= FALSE,错误= FALSE,整洁= FALSE) #关掉冗长BiocStyle:::乳胶 () ## ---- 选项,包括= FALSE ------------------------------------------------ ## 选项(错误=恢复,警告= 2)选项(bitmapType = "开罗 ") ## ---- DataLoading ----------------------------------------------------------- 库(“ALLMLL”)(“MLL.A数据 ") ## ---- AffyBatchQM,结果=“隐藏 "------------------------------------------- 库(arrayQualityMetrics) arrayQualityMetrics (expressionset = MLL。A[， 1:5]， outdir = "Report_for_MLL_A"， force = TRUE, do。logtransform = TRUE) # #——正常化,结果=“隐藏 "----------------------------------------- nMLL = rma (MLL.A) # #——ExpressionSet --------------------------------------------------------- arrayQualityMetrics (expressionset = nMLL outdir =“Report_for_nMLL”,力= TRUE) # #——NChannelSet1,结果= "隐藏 "------------------------------------------ 库(vsn)图书馆(“亚兰”)的数据(“亚兰”)nCCl4 = justvsn(亚兰,子样品= 15000)arrayQualityMetrics (expressionset = nCCl4,outdir = " Report_for_nCCl4”,力= TRUE) # #——intgroup1 ------------------------------------------------------------- pData (nMLL)条件美元=代表(字母[1:4]* = 5)pData (nMLL)批美元=代表(粘贴(1:4),每个= 5)# #——intgroup2 ------------------------------------------------------------- arrayQualityMetrics (expressionset = nMLL outdir =“Report_for_nMLL_with_factors”,迫使= TRUE, intgroup = c(“条件”,“批 ")) ## ---- XYcoordinates --------------------------------------------------------- featureData (nCCl4) $ X = featureData (nCCl4)美元行featureData (nCCl4) $ Y = featureData (nCCl4) $ # #——hasTarget列 ------------------------------------------------------------- featureData (nCCl4) $ hasTarget = (regexpr(“^海里”,featureData (nCCl4)名称)> 0美元)表(featureData (nCCl4) hasTarget美元)# #——pData ----------------------------------------------------------------- pd = pData(亚兰)rownames零帕金森病(pd) = # #——RIN ------------------------------------------------------------------- RIN = (pd, ifelse (RIN Cy3 = =“亚兰”。Cy3 RIN.Cy5)) fRIN =因素(RIN)水平(fRIN) = c(“可怜”,“中”,“好”)pData (nCCl4)“RNA-integrity”=美元fRIN # #——NChannelSet2 ---------------------------------------------------------- arrayQualityMetrics (expressionset = nCCl4 outdir =“Report_for_nCCl4_with_RIN”,迫使= TRUE, intgroup = " RNA-integrity ") ## ---- 包裹,回声= FALSE,结果= "飞机 "-------------------------------------- toLatex (sessionInfo ())