[BioC] expression set and paired designs
David martin
vilanew at gmail.com
Mon Dec 7 14:35:30 CET 2009
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
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