Hi, Pepin and Jim
  Thank Pepin and Jim for your help.
  But I haven't still figured out. After installing affycoretools, annaffy, Gostats and copy your code, I thought it was working but I got the following message. 
  ## error in "data frame" undefined column specified ## 
  I am afraid I made a mistake somewhere. Because I am so new to this statistic analysis area, could you help me to find what I did wrong? Also could you tell me what exactly the program use to do the calculation to get the number of genes? For example, "ID" for my individual spot identification, or "Acession" for gene identification from my annotation list.
  Thanks again.
   
  Sincerely, Seungmin Lee
   
  library(affycoretools)
ups <- affycoretools:::makeIndices(results, "up")
downs <- affycoretools:::makeIndices(results, "down")
  up.genes <- lapply(ups, function(x) row.names(results)[x])
  down.genes <- lapply(downs, function(x) row.names(results)[x])
  

Francois Pepin <fpepin@cs.mcgill.ca> wrote:
  Hi Jim,

you are correct, my code only looks at one contrast at a time, the same
way that topTable does it. Your modification is needed to look at the
intersection.

Francois

On Wed, 2006-11-01 at 14:36 -0500, James W. MacDonald wrote:
> Hi Francois,
> 
> Francois Pepin wrote:
> > Hi Seung-Min,
> > 
> > The differences come from the classifyTestsF. It classifies the genes
> > based on the F statistics, rather than the B-values which topTable uses.
> > 
> > Another way to get the information about the up genes both contrast
> > (Jim's way should work too):
> > 
> > fit$genes[which(results[,1]>0,] ##set to <0 for down genes
> 
> I don't think that will work. The first column of the results matrix 
> gives information about the genes in the first contrast only. To get 
> both contrasts, you need results[,1] > 0 & results[,2] > 0. In any case, 
> you have to look at both contrasts to find the genes for any given cell 
> of the Venn diagram.
> 
> Best,
> 
> Jim
> 
> 
> > 
> > Please note that, unlike topTable, the list is ordered by position on
> > the chip, not by how significant the differences are.
> > 
> > Francois
> > 
> > On Tue, 2006-10-31 at 16:25 -0800, lee wrote:
> > 
> >>Hello,
> >> I am using my two color array data. I want to know the genes that
> >>are significantly Up or Down in both "HFEvsWT" and "SlavsWT" groups
> >>from Venn diagram results. I also want to know the genes that are only
> >>significantly Up or Down in one group. When I tried using the gene
> >>list from topTable function, I got different number of genes compared
> >>to Venn Diagram results. Thus, I want to know what are the genes after
> >>Venndiagram analysis.
> >> Could you help me?
> >> Thank you so much.classifyTestsF
> >> 
> >> Sincerely, Seungmin Lee
> >> 
> >> 
> >> 
> >> 
> >> library(limma)
> >>targets<-readTargets("Target4wkEnteroHFESla.txt")
> >>f<-function(x) as.numeric(x$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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> >>
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> >>
> > 
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
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> 
> 




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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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