Dear Thanh Le,
Please remember to post your questions to the entire Bioconductor 
list.  You can always send a cc to the person you think can answer 
it, but if you post to the list

a) someone else might find the answer sooner (and when I get busy, I 
sometimes do not answer Bioconductor questions for weeks)
b) everyone on the list will see the response

You can do the contrasts the way you have set it up here, but there 
are 2 problems:

a) You will need to drop the intercept from the model.
b) Without replication no statistical routine including limma can do 
a statistical test.  So, if you have only 2 cel files, there is no 
point in running limma.  Just look at the fold difference.

Sincerely
Naomi



At 06:39 PM 6/4/2008, you wrote:
>Dear Professor Naomi Altman,
>
>I am THANH LE, a student of the Univ. of Colorado.
>
>Could you please help me on a problem of gene expression analysis.
>Assume I have two CEL files from an experiment: A and B where A is 
>the control and B is the treatment with a drug. I would like to 
>extract genes which are differentially expressed from this 
>experiment. I used limma from R software with the following two matices:
>
>Design matrix: D
>
>C   T
>1   0
>0   1
>
>Contrasts matrix:
>
>c<-makeContrasts(C-T,levels=D)
>
>Could you please tell me if the two matrices are correct to my experiment?
>
>Thank you for reading and answering my email.
>
>Best regards,
>Thanh Le

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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