Dear All,

I was trying to analyse the GEO data from GSE format


Following is the code

gse <- getGEO('gse6901')[[1]]
exprs(gse)
log2(exprs(gse))
set <- log2(exprs(gse))
target <- c('A','A','A','B','B','B','C','C','C','D','D','D')
f <- factor(targets,levels=c('A','B','C','D'))
design <- model.matrix(~0+f)
contrast.matrix <- makeContrasts(fA-fB,fA-fC,fA-fD,levels=design)
fit <- lmFit(set,design,method="robust")
fit2 <- contrasts.fit(fit,contrast.matrix)
fit2 <- ebayes(fit2)


I am ineterested in log fold change between the contrast samples, but the as
I see it is not there

my question is how can i get the log fold change between the contrast
samples

I shall be very thankful for any help and suggesstion

Regards

Hemant

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