[BioC] permutation

James W. MacDonald jmacdon at med.umich.edu
Thu Dec 2 21:02:12 CET 2010

Hi Peevi,

On 12/2/2010 2:51 PM, Steve Lianoglou wrote:
> Hi Peevi,
> Please keep all correspondence on the list as other people will be the
> ones helping you with this.
> Your response is below:
> On Thu, Dec 2, 2010 at 2:46 PM, Peevi Ijkl<ipeevi at yahoo.com>  wrote:
>> hello steve
>> this is wot i did so far..
>> load the cel files..gcRMA..nonspecific filtering..then GeneSetCollection foe
>> KEGG..constructed an incidence matrix..computed per gene test statistics
>> using rowttest function..Compute the Z score for  each pathway..now i want
>> to do permutation using library(Category) and list pathways with p value cut
>> off  .05 .

I believe this is covered on page 7 of the Category vignette:




> But sorry .. I'm not really sure what you're trying to do, and can't
> spend much time trying to.
> I was hoping your exposition would provide more information that
> others can use to help you with.
> -steve

James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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