[R] vectorizing ANOVA over a vectorized linear model

hadley wickham
Sun, 07 Mar 2010 19:08:11 -0000

Hi Mark,

If efficiency is a concern you might want to read "Computing Thousands
of Test Statistics Simultaneously in R" by Holger Schwender and Tina
M?ller, http://stat-computing.org/newsletter/issues/scgn-18-1.pdf.

If you just want to do it, see the examples in
http://had.co.nz/plyr/plyr-intro-090510.pdf.

Hadley

On Sun, Mar 7, 2010 at 7:03 PM, Mark Kimpel <mwkimpel at gmail.com>
wrote:
> Is it possible to vectorize anova over the output of a vectorized lm? ?I
> have a gene expression matrix with each row being a gene and columns for
> samples. There are several factors with interactions. I can get p values by
> looping over the matrix with lm and anova, but I would like to make this as
> computationally efficient as possible. I am able to vectorize the lm
> command, but when I try to use anova on the resultant model object I get
> just one anova result.
>
> Is what I want to do possible? And, yes, I am quite conversant with Limma
> and other BioC packages, I have my reasons for wanting to use lm and anova.
>
> Thanks,
>
> Mark
> Mark W. Kimpel MD ?** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN ?46074
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--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University