[BioC] 2 way anova in Bioconductor

[axel.klenk at actelion.com]

Hi Dana,

limma can do that easily. The current version of the user's guide
contains one chapter and two case studies on 2x2 factorial designs.

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland





From:
<Dana.Stanley at csiro.au>
To:
<bioconductor at r-project.org>
Date:
28.06.2011 03:27
Subject:
[BioC] 2 way anova in Bioconductor
Sent by:
bioconductor-bounces at r-project.org



Hi Everyone

I use custom designed chicken high-density multiplex one channel 
microarray (NimbleGen 12x135K). My usual pipeline includes mostly oligo, 
arrayQualityMetrics, preprocessCore, genefilter, GeneSelector and limma. 
So far I only worked with simple design, 2 conditions; control/treatment 
style. Now I have a dataset with embryonic development timeline for male 
and female chicks. I still compare different timepoints using limma but I 
want to do 2 way anova to identify interaction significant genes, ie genes 
where gender influences development timeline. I looked at many packages 
and could not find 2 way anova, though I am sure it is there somewhere. I 
tested package ABarray that seemed ideal for my me but after days of 
trying I contacted the author to find out that expression sets (mine is 
coming  from limma) can no longer be used by ABarray  as the package has 
not been updated for a while.  Can anyone suggest a package (and an 
example code if possible) for 2 way anova? I am so temp!
 ted to go and do it in GeneSpring...

Thanks all

Dana


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