
Dear all,
I have 4 samples of HT 430mgpm array plate. Three of them are replicates of wild types and 1 is a tumor condition with no replicates. But I do not have any other information regarding how was the experiment conducted and I am not able to figure out how to create a phenodata of the same. When I create the expression set of this data using rma function of affy library I can see the names of the samples as they were and sample numbers namely 1,2,3,4. What I understand is it takes alll the four samples as different and when I do the differential expression analysis using limma , I try to create the model.matrix using the following command : 
 
design <- model.matrix(~sample, pData(eset))

But what I understand is that the sample that are present in the data it is taking 1 condition each of 4 samples. Am I understanding it correctly?.
If so what should I be doing to get differential expression of genes in tumor as compare to the 3 wild type replicates that I have . 

I am very new to this field and so I am not sure how to proceed 
Any help will be much appreciated.
Thanks ,
Himanshu Sharma.
 		 	   		  
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