# # # R代码从装饰图案的spkDoc来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:spkDoc。Rnw: 229 - 230 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(spkTools) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:spkDoc。Rnw: 233 - 235 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据对象(affy) <——affy # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:spkDoc。Rnw: 239 - 242 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fc = 2标签=“Affymetrix par (mar = c (3、2.5、2、0.5), cex = 1.8) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:spkDoc。Rnw: 249 - 250 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # spkSlopeOut <——spkSlope(对象、标签、pch = " + ") # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:spkDoc。Rnw: 264 - 265 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # spkDensity(对象、spkSlopeOut削减= TRUE,标签)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:spkDoc。Rnw: 278 - 281 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # spkBoxOut < - spkBox(对象、spkSlopeOut fc) plotSpkBox (fc, spkBoxOut ylim = c (-1.5, 2.5)) sbox <——summarySpkBox (spkBoxOut) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:spkDoc。Rnw: 297 - 298 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # spkMA(对象、spkSlopeOut fc,标签=标签,ylim = c(-2.5, 2.5)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:spkDoc。Rnw: 316 - 330 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # vtmp < - spkVar(对象)sv < - as.numeric (vtmp [2] [-nrow (vtmp)])本< - c(“低”、“地中海”、“高”)垃圾箱< -本[spkSlopeOut打破美元[2]]tab1 < - data.frame (NominalConc = 2 ^ spkSlopeOut打破美元[1],AvgExp =圆(spkSlopeOut AvgExp美元,1),PropGenesBelow =圆(spkSlopeOut支撑美元,2),ALEStrata =垃圾箱,SD =圆(sv, 2)) colnames (tab1) < - c(“浓缩的名义”、“Avg表达”,“下面支撑的基因”,“啤酒阶层”,“Std Dev”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:spkDoc。Rnw: 333 - 336 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(xtable) tab1x <——xtable (tab1)打印(tab1x) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:spkDoc。Rnw: 352 - 366 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # AccuracySlope < -轮(spkSlopeOut斜坡[1]美元,数字= 2)AccuracySD < -轮(spkAccSD(对象,spkSlopeOut),数字= 2)锅< - spkPot(对象、spkSlopeOut AccuracySlope、AccuracySD precisionQuantile = .995) PrecisionSD < -轮(sbox madFC美元[1:3],数字= 2)precisionQuantile < -轮(锅分位数美元,数字= 2)信噪比< -轮(AccuracySlope / PrecisionSD位数= 2)锅< -轮(锅锅美元,数字= 2)tab2 <——data.frame (AccuracySlope = AccuracySlope AccuracySD = AccuracySD PrecisionSD = PrecisionSD precisionQuantile = precisionQuantile,信噪比=信噪比,锅=锅)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:spkDoc。Rnw: 368 - 370 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # tab2x <——xtable (tab2)打印(tab2x) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:spkDoc。Rnw: 392 - 395 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #巴尔斯< -轮(spkBal(对象)anv < -轮(spkAnova(对象),数字= 2)tab3 < - t (c (anv,巴尔斯))# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:spkDoc。Rnw: 397 - 399 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # tab3x < - xtable (tab3)打印(tab3x)