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

[shirley zhang]

Hi Naomi,

Thank you so much for your help. I also remember you gave me some very
helpful suggestions regarding Quantile Normalization aross different
tissues a few days ago. Thanks again.

Again for this issue, can limma handle mixed effect model like lme? I
can only do paired test with Limma, but here each subject has 3
tissues.

Thanks,
Shirley

On 6/6/07, Naomi Altman <naomi at stat.psu.edu> wrote:
> 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
>
>