[BioC] anova and multiple comparisons

[Naomi Altman]

I would use limma followed by qvalue (another Bioconductor package).  There 
are several examples on this mainling list of how to set this up.  Check my 
message of yesterday for a comment about the correspondance between SAM and 
limma for 1-way ANOVA.

-Naomi

At 10:28 AM 6/25/2004 -0500, Kimpel, Mark W wrote:
>I have been using SAM to estimate FDR when performing multiple
>comparisons on two groups. I have now been tasked with performing a
>similar analysis on a 2X2 experiment (2 groups each with two
>treatments). For a single comparison, ANOVA would be the obvious choice.
>What should be my approach for multiple (about a thousand) comparisons?
>
>Thanks,
>
>Mark W. Kimpel MD
>
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111