Hello,
  I am using my two color array data. I want to know the genes that are significantly Up or Down in both "HFEvsWT" and "SlavsWT" groups from Venn diagram results. I also want to know the genes that are only significantly Up or Down in one group. When I tried using the gene list from topTable function, I got different number of genes compared to Venn Diagram results. Thus, I want to know what are the genes after Venndiagram analysis.
  Could you help me?
  Thank you so much.
   
  Sincerely, Seungmin Lee
   
   
   
   
  library(limma)
targets<-readTargets("Target4wkEnteroHFESla.txt")
f<-function(x) as.numeric(x$Flags>-99)
files<-targets[,c("FileName")]
RG<-read.maimages(files,columns=list(R="F635 Mean",G="F532 Mean",Rb="B635 Median",Gb="F532 Median"),annotation=c("Block","Row","Column","ID","Accession","Symbol"))
  plotMA(RG)
RG$genes<-readGAL("meebo.gal")
RG$printer<-getLayout(RG$genes)
  MA.p<-normalizeWithinArrays(RG,method="loess")
MA.pAq<-normalizeBetweenArrays(MA.p,method="Aquantile")
design<-modelMatrix(targets,ref="WT.C57.chow")
design
contrast.matrix<-cbind("HFEvsWT"=c(1,0),"SlavsWT"=c(0,1))
rownames(contrast.matrix)<-colnames(design)
contrast.matrix
fit<-lmFit(MA.pAq,design)
fit2<-contrasts.fit(fit,contrast.matrix)
fit2<-eBayes(fit2)
  topTable(fit2,coef="HFEvsWT",adjust="BH")
plotMA(fit2,array=1)
  topTable(fit2,coef="SlavsWT",adjust="BH")
plotMA(fit2,array=2)
  results<-classifyTestsF(fit2, p.value=0.01)
summary(results)
table("HFEvsWT"=results[,1],"SlavsWT"=results[,2])
vennDiagram(results,include="up")
vennDiagram(results,include="down")


-----------------------------------------------------------------------
Seung-Min Lee

graduate student
244 Morgan Hall
Molecular&Biochemical Nutrition
University of California at Berkeley
94720-3104
lab phone (510)643-2351
lab fax(510)642-0535

 
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