[BioC] question_gene list from venn diagram limma function for two color array data

[Francois Pepin]

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

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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