[BioC] Fold change GEO data

[Sean Davis]

On Tue, Sep 9, 2008 at 6:05 AM, hemant ritturaj
<ritturajhemant at gmail.com> wrote:
> 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

Hi, Hemant.  When posting code, it is best to cut-and-paste it from
you session to avoid typos (target should be targets above).

When you say "I see it is not there", I'm not sure what you mean.
Have you looked at the topTable output (you'll have to read the limma
user guide and topTable help)?  If you have done that, then could you
complete your example and explain what is missing?

Hope that helps.

Sean