Dear Chen,

You need not to look for any other packages. Since, you do not have any replicates, do not fit linear model, instead just do normalization with in arrays and look at the M (log ratio) values.

Regards,

Prashantha Hebbar Kiradi,

Dept. of Biotechnology,

Manipal Life Sciences Center,

Manipal University,

Manipal, India



--- On Mon, 1/25/10, Chuming Chen <chumingchen@gmail.com> wrote:

From: Chuming Chen <chumingchen@gmail.com>
Subject: [BioC] Agilent G4112A Arrays
To: bioconductor@stat.math.ethz.ch
Date: Monday, January 25, 2010, 6:32 AM

Dear All,

I am trying to find out the differentially expressed genes from some Agilent Human Whole Genome (G4112A) Arrays data.

I have tried LIMMA package, but LIMMA gave the error message "no residual degrees of freedom in linear model fits" and stopped. My guess is that my data has no replicates in the experiment.

Is there any other packages I can use to find differentially expressed genes which does not require replicates in the experiment?

Thanks for your help.

Chuming

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