Dear Sean,

My apologies for the errror.

Here I am giving the complete error which i am getting

> gse <- getGEO('gse6901')[[1]]
> exprs(gse)
> log2(exprs(gse))
> set <- log2(exprs(gse))
> targets <- 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)

> names(fit2)
[1] "df.prior"  "s2.prior"  "s2.post"   "t"         "p.value"   "var.prior"
[7] "lods"

topTable(fit2,n=10)
Error in if (ncol(fit) > 1) return(topTableF(fit, number = number, genelist
= genelist,  :
  argument is of length zero


I am not able to figure out logFC from the contrast matrix.

also using the topTable gave me the above error.

Also I am not able to understand why there are lesser variables than doing
the same kind of analysis done using raw cel microarray files. Am I missing
some things in my program ?? or it is the limitation using NCBI-GEO GSE
format files.

I am pasting one of the variable results done from the raw cel microarray
files for your kind refernce

names(fit2)
 [1] "coefficients"     "rank"             "assign"
"qr"
 [5] "df.residual"      "sigma"            "cov.coefficients"
"stdev.unscaled"
 [9] "genes"            "Amean"            "method"
"design"
[13] "contrasts"        "df.prior"         "s2.prior"
"var.prior"
[17] "proportion"       "s2.post"          "t"
"p.value"
[21] "lods"             "F"                "F.p.value"

Thanks  for  helping

Regards

On Tue, Sep 9, 2008 at 8:11 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Tue, Sep 9, 2008 at 6:05 AM, hemant ritturaj
> <ritturajhemant@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
>



-- 
Hemant Ritturaj Kushwaha
PhD Student
Center for Computational Biology and Bioinformatics
Jawaharlal Nehru University
New Delhi-110067
Phone: 09868801604

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