[BioC] Can subject be treated as fixed effect in linear model with microarray data

[Naomi Altman]

Model 3 is completely illegal.  Model 2 is sometimes used when there 
are few within subject observations (as here).  However, I would not 
do that here.  I would use an eBayes method such as limma to improve power.

--Naomi

At 11:34 AM 6/5/2007, shirley zhang wrote:
>Dear Bioconductor,
>
>In a microarray data, there are 20 subjects grouped by Gender, each
>subject has 2 tissues (normal vs. cancer).
>
>In fact, it is a 2-way anova (factors: Gender and tissue) with tissue
>nested in subject. I've tried the following:
>
>Model 1: lme(response ~ tissue*Gender, random = ~1|subject)
>Model 2: response ~ tissue*Gender + subject
>Model 3: response ~ tissue*Gender
>
>
>It seems like Model 1 is the correct one since my experiment design is
>nested design. However, I got a few significant genes for Gender
>effect from Model 1 so I want to use Model 2 or Model 3. Can anybody
>tell me whether Model2 is
>completely illegal?
>
>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