Entering edit mode
> Date: Wed, 7 Jun 2006 12:06:13 -0700 (PDT)
> From: Vijay A Raghavan <rva_ec at="" yahoo.com="">
> Subject: [BioC] decideTest extraction of P values
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <20060607190613.54736.qmail at web53514.mail.yahoo.com>
> Content-Type: text/plain
>
> Hello all,
>
> Here is the code that I am using for finding differentially
expressed genes.
>
> #Normalization
>
> library(affy)
> library(Biobase)
> library(limma)
> library(gcrma)
>
> pd<-read.phenoData("file.txt",header=TRUE,row.names=1,as.is=TRU
E,sep="\t")
> Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)
> print(Data)
>
> eset <- gcrma(Data)
> write.exprs(eset, file="decide-test.6-6-06.txt")
>
> #Linear Model
>
> pData(eset)
> targets<-pData(eset)
> model.matrix(~ -1
+factor(targets$Target,levels=unique(targets$Target)))
> design <- model.matrix(~ -1 +
> factor(targets$Target,levels=unique(targets$Target)))
> unique(targets$Target)
> colnames(design) <- unique(targets$Target)
> ncol(design)
> numParameters <- ncol(design)
> colnames(design)
> parameterNames <- colnames(design)
> design
> fit <- lmFit(eset,design=design)
> names(fit)
>
> contrastNames
<-c(paste(parameterNames[2],parameterNames[1],sep="-"),
> paste(parameterNames[3],parameterNames[1],sep="-"),
> paste(parameterNames[4],parameterNames[1],sep="-"),
> paste(parameterNames[5],parameterNames[1],sep="-"),
> paste(parameterNames[6],parameterNames[1],sep="-"),
> paste(parameterNames[7],parameterNames[1],sep="-"))
>
> contrastsMatrix <- matrix(c(
> -1,1,0,0,0,0,0,
> -1,0,1,0,0,0,0,
> -1,0,0,1,0,0,0,
> -1,0,0,0,1,0,0,
> -1,0,0,0,0,1,0,
> -1,0,0,0,0,0,1),nrow=ncol(design))
> rownames(contrastsMatrix) <- parameterNames
> colnames(contrastsMatrix) <- contrastNames
> contrastsMatrix
>
> fit2 <- contrasts.fit(fit,contrasts=contrastsMatrix)
> names(fit2)
>
> #ebayes
>
> fit2 <- eBayes(fit2)
> names(fit2)
> numGenes <- nrow(eset at exprs)
>
> #decideTest
>
> results <- decideTests(fit2,method="nestedF",p=0.05);
> write.fit(fit2, results, "data.txt", adjust="BH");
>
>
> Is there any way for getting the adjusted p-values from the
decideTests method ?
>
> Thanks,
>
> Vijay
> [[alternative HTML version deleted]]
p.adjust(fit2$F.p.value,method="BH")
Best wishes
Gordon
