[BioC] expression set and paired designs

[David martin]

Hi,
Here is the experimental design (done by flow cytometry).

Collect sample from a set of patients-> measure the expression for a set 
of genes in different celltypes from the same sample.

So the normalized data look like that:

	celltype(1 or2)	geneA	geneB	geneC
patient1	1	40	20	40
patient1	2	37	18	41
patient2	1	40	19	38
patient2	2	38	17	39
patient3	1	10	19	38
patient3	2	20	17	39

....(n)


and then i have my pdata.txt.

Sample	Disease_stage
patient1	moderate_disease
patient2	severe_disease
patient3	normal


What i want to do is to compare the different groups and identify the 
genes that differentially expressed between the three groups.
That i guess would be fine to do by bulding a proper design and runing a 
paired t.test.


But before that I can't construct an eset object as sample names are 
duplicates. I was wondering if i need to construct two eset objects (one 
for celltype1 and one for celltype2) ???

Any help would be appreciated.

thanks