[BioC] expression set and paired designs
David martin
vilanew at gmail.com
Mon Dec 7 16:43:20 CET 2009
Is there any simple example to start with ?
Naomi Altman wrote:
> What you have is a split plot design.
>
> The whole block factor is disease severity. The blocks are patients.
> The subplot factor is cell type.
>
> Since there are only 2 cell types, you can readily determine the disease
> by cell type main effect, by analyzing the differences between the cell
> types for each
> patient. However, if the main effects are also of interest, you need to
> run the split plot design ANOVA for each gene.
>
> I am not sure whether you can do this in Limma, using patient as block.
> If not, you should be able to do it in MAANOVA.
>
> --Naomi
>
> At 08:35 AM 12/7/2009, David martin 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) ???
>>
>> Any help would be appreciated.
>>
>> thanks
>>
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>
> 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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