[BioC] expression set and paired designs

[Sean Davis]

On Mon, Dec 7, 2009 at 8:35 AM, David martin <vilanew at gmail.com> wrote:
> 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) ???

I would suggest thinking of a "patient" as a source for a sample, and
not the sample itself, in the most general of terms.  In other words,
label your samples 1..2n (if you have two samples per patient) and
then connect the sample ids with the patient ids in the phenoData of
the ExpressionSet.  Does that make sense?

Sean