[BioC] expression set and paired designs

[David martin]

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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