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 M. Srikanth
Ph.D. Student
Institute of Bioinformatics
Discoverer, 7th Floor,
International Technology Park,
Bangalore, India
Mob:+919019114878

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