[BioC] Finding differentially expressed genes using Ebayes

John Herbert j.m.herbert at bham.ac.uk
Mon May 11 13:53:11 CEST 2009

I have 6 gpr files, 3 from cancer and 3 from normals. I have normalised them with printtiplowess and removed the control spots. My question is about finding differentially expressed genes with Ebayes. I have run the code below and get some strange results that are very different to using Samr. I am thinking I trust samr more as when I look at the results by eye, they seem to order the genes coffectly based on fold ratio. However, it could be that I am not using ebayes correctly. 

So, the design is supposed to represent cancer (the 1s) and normal (the 2s). Is this the correct way to construct a design matrix? I want to compare gene expression between cancer and normal (3 replicates each).  

design <- model.matrix(~factor(c(1,1,1,2,2,2)));

fit <- lmFit(probes_only.imp, design);

fit <- eBayes(fit);

probes_only.imp_50_ebayes <- topTable(fit, n=20);

Any help appreciated on this, thank you. 

Kind regards,


Bioinformatics Officer

Molecular Angiogenesis group
First Floor, Institute of Biomedical Research
The University of Birmingham
Medical School
B15 2TT  (UK)

j.m.herbert at bham.ac.uk

Tel:  +44 121 414 3733
Fax: +44 121 415 8677 

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