[BioC] Query regarding limma

[Gordon K Smyth]

By using write.fit().

Best wishes
Gordon

> Date: Tue, 29 Jan 2013 18:05:30 -0500
> From: Roopa Subbaiaih <rss115 at case.edu>
> To: bioconductor at r-project.org
> Subject: [BioC] Query regarding limma
>
> Hi All,
>
> I was doing microarray analysis where I compare healthy with diseased
> samples. The script which I use is
>
> getwd()
> setwd(dir="/CRSP 406-11/DEMOS/GSE14905-a")
> ls()
> #-----------------------------------------------#
> library(affy)
> eset = justRMA()
> f <- factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
>
> 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2),
> labels=c("Healthy", "unaffected"))
> design <- model.matrix(~ 0 + f)
> design
> colnames(design) <-c("Healthy","unaffected")
> design
> library(limma)
> fit <- lmFit(eset, design)
> library(hgu133plus2.db)
> fit$genes$Symbol <- getSYMBOL(fit$genes$ID,"hgu133plus2.db")
> contrast.matrix <-makeContrasts(affected-Healthy,levels = design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> topTable(fit2,coef=1,p=0.05, adjust="fdr")
> results <- decideTests(fit2, adjust="fdr", p=0.05)
> summary(results)
> write.table(results,file="myresults.txt")
>
> The results table shows ~10,000 genes to be upregulated and ~12,000 genes
> to be down regulated.
>
> My question is how can I get fold change values associated with these genes
> in the results file?
>
> Thanks in advance, Roopa
>

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