# # # R代码从装饰图案来源的简述。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:简述。Rnw: 108 - 109 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # packageDescription(简述)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:简述。Rnw: 118 - 119 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # set.seed(0) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:简述。Rnw: 123 - 124 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(简述)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:简述。Rnw: 134 - 138 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(雷)暗(雷)头(雷)雷。子集< -雷(seq(1000)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:简述。Rnw: 155 - 158 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #雷。规范化< -雷。雷子集。归一化[2:7]< -预处理(雷。[2:7],数据子集。type = " MAS5”)雷。归一化[1:3],# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:简述。Rnw: 163 - 166 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #雷。最后< - Ley.normalized (substring (Ley.normalized $ ID、1, 4) ! =“AFFX]暗雷(Ley.final)。最后[1:3]# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:简述。Rnw: 175 - 178 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # var.Naive <——baseOlig.error (Ley.final [2:4], q = 0.01)暗(var.Naive) var.Naive[1:3], # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:简述。Rnw: 184 - 187 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # var.Activated < baseOlig.error(雷。final[,5:7], q=0.01) dim(var.Activated) var.Activated[1:3,] ################################################### ### code chunk number 9: LPE.Rnw:198-206 ################################################### lpe.val <- data.frame(lpe(Ley.final[,5:7], Ley.final[,2:4], var.Activated, var.Naive, probe.set.name=Ley.final$ID) ) lpe.val <- round(lpe.val, digits=2) dim (lpe.val) lpe.val[1:3,] ################################################### ### code chunk number 10: LPE.Rnw:219-222 ################################################### fdr.BH <- fdr.adjust(lpe.val, adjp="BH") dim(fdr.BH) round(fdr.BH[1:4, ],2) ################################################### ### code chunk number 11: LPE.Rnw:231-233 ################################################### fdr.resamp <- fdr.adjust(lpe.val, adjp="resamp", iterations=2) fdr.resamp ################################################### ### code chunk number 12: LPE.Rnw:249-251 ################################################### Bonferroni.adjp <- fdr.adjust(lpe.val, adjp="Bonferroni") head(Bonferroni.adjp)