Hi all, I am working with two color microrray data and have three different stages of cancer along with normal, all normalized with a universal Normal. I analyzed the data using Limma package in R.My workflow is as below: library(limma) targets<-readTargets(filename) RG<-read.maimages(targets,source="genepix") RG$genes<-readGAL() MA<-normalizeWithinArrays(RG,method="loess") plotMA(RG) plotMA(MA) MA<-normalizeBetweenArrays(MA,method="aquantile") design=modelMatrix(MA,ref="Control") fit<-lmfit(MA,design) fit2<-ebayes(fit) contrastmatrix<-makeContrasts("StageI-Normal","StageII-Normal ","StageIII-Normal","StageIII-StageI","StageII-StageI","StageIII- StageII",levels=design) fit3<-contrasts.fit(fit2,contrastsmatrix) fit3<-ebayes(fi3) results <- decideTests(fit3,method="global") vennDiagram(results[,1:3]) I want to print the common genes which are common in all three stages and also find common signature set of genes among different stages, please help on how I should proceed further. The target file is as below: SampleNumber FileName Cy3 Cy5 1 CN 310_N.gpr Control Normal 2 CN 314_N.gpr Control Normal 3 CN 318_N.gpr Control Normal 4 CN 321_N.gpr Control Normal 5 CN 322_N.gpr Control Normal 6 CT 1015_II.gpr Control StageII 7 CT1021_II.gpr Control StageII 8 CT 1063_II.gpr Control StageII 9 CT1077_II.gpr Control StageII 10 CT1099_III.gpr Control StageIII 11 CT 1131_III.gpr Control StageIII 12 CT 1138_I.gpr Control StageI 13 CT 1178_III.gpr Control StageIII 14 CT 1179_III.gpr Control StageIII 15 CT 1187_III.gpr Control StageIII 16 CT500_I.gpr Control StageI 17 CT503_II.gpr Control StageII 18 CT 510_I.gpr Control StageI 19 CT 513_I.gpr Control StageI 20 CT 514_I.gpr Control StageI 21 CT 515_I.gpr Control StageI 22 CT 800_II.gpr Control StageII 23 CT 805_II.gpr Control StageII 24 CT 809_III.gpr Control StageIII 25 CT 833_I.gpr Control StageI 26 CT 843_I.gpr Control StageI 27 CT 859_III.gpr Control StageIII 28 CT 871_II.gpr Control StageII 29 CT 905_III.gpr Control StageIII 30 CT 935_II.gpr Control StageII Regards, Srikanth -- Srinivas Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+919019114878, India [[alternative HTML version deleted]]

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