[BioC] 2 way anova in Bioconductor

[mjonczyk at biol.uw.edu.pl]

Dear Dana,

you can try maanova package. I haven't use it extensively but as I know it can
handle 2-way anova as well as more complicated designs.
Details and examples could be found on developers' page, given at package page:
http://www.bioconductor.org/packages/release/bioc/html/maanova.html.

HTH,
Maciej


> Date: Tue, 28 Jun 2011 11:26:40 +1000
> From: <Dana.Stanley at csiro.au>
> To: <bioconductor at r-project.org>
> Subject: [BioC] 2 way anova in Bioconductor
> Message-ID:
>	<605D22ED4C355C44AE8703F8787832BFB11F40D276 at EXVIC-MBX02.nexus.csiro.au>
>	
>  
> 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