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

	[[alternative HTML version deleted]]

