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

[James W. MacDonald]

Hi Seungmin,

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.
>    
>   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")

The affycoretools package is designed for analysis of one-color chips, 
but you could use a utility function from that package to do what you want.


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])

Now you will have two lists each containing the gene names corresponding 
to the left, right, and intersection of your Venn diagrams.

You could also use the 'ups' and 'downs' lists to extract information 
from your fit2 object such as t-statistics or p-values, etc.

HTH,

Jim


> 
> 
> -----------------------------------------------------------------------
> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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