[BioC] 2-way Anova analysis

James W. MacDonald jmacdon at med.umich.edu
Thu Jan 5 18:40:49 CET 2006

Sharon wrote:
>  Hi All,
> I am trying to analyze affy data for strain, treatment and their interaction
> effects (RMA normalized, log2 expression values). The design looks like
>    strain A --> treatment 1       strain B --> treatment 1
>                     treatment 2                         treatment 2
> so, I used anova(aov(expra ~ strain + treatment + strain*treatment, m)),
> where m <- data.frame(strain, treatment, expr)
> I have got the corresponding pvalues for strain, treatment & interaction
> effects( this for all the probsets).  Now, I would like to separate the
> number of significant probesets for strain A and strain B from strain effect
> (I would like to do the same for treatment effect).  How can I do this? Any
> help is very much appreciated.

I am not sure exactly what you are asking for here, but you are probably 
better off using the limma package. After fitting the model you can then 
use e.g., decideTests() and vennDiagram() to get the number of probesets 
significant in contrasts of interest.

There is an excellent User's Guide that accompanies this package that 
will answer about 90% of the questions you may have.



> Thanks in Advance.
> Regards,
>  Sharon
> 	[[alternative HTML version deleted]]
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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