[BioC] anyway to speed up anova on every row of a 280k-row matrix

[Robert Gentleman]

if the design matrix is constant then there are all sorts of way to speed things
up. Using apply is probably the worst thing you could do...
have a look at GSEAlm for some ways to compute fits, residuals and other
diagnostics quickly.

best wishes
 Robert


Kasper Daniel Hansen wrote:
> Use limma, as you are supposedly fitting the same model to every row.
> 
> Kaspr
> 
> On Apr 7, 2009, at 8:12 , Zheng, Xin (NIH) [C] wrote:
> 
>> Hi there,
>>
>> I was doing anova on an array file. I know Partek can do it in
>> minutes, yet it cost half an hour in R with apply(matrix, 1, function
>> of anova). Any hint? Thanks.
>>
>> Xin Zheng
>>
>>
>>     [[alternative HTML version deleted]]
>>
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org