[BioC] factorial analysis of affy arrays

[Arne.Muller at sanofi-aventis.com]

Hello,

look at the limm package and browse the lists archive for postings/questions on limma. It's a linear model that adjusts variance via other genes on the chip (I hope I got this right ...) and probably performs better than "lm/anova". It's one of the most frequently used packages for finding differentially expressed genes. It also works single and two channel arrays.

	Arne

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Jakub
> Orzechowski
> Sent: 08 February 2005 11:21
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] factorial analysis of affy arrays
> 
> 
> Hi! I'm doing some experiments with affy arrays, with a 2*2*2 
> factorial 
> design. Which tools are available for analysis of such experiments? 
> Which methods can you recomended? What about ANOVA stuff from 
> YASMA? Any 
> other suggestions?
> 
> thanks
> Jakub Orzechowski
> 
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