[BioC] permutation

[James W. MacDonald]

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:

http://www.bioconductor.org/packages/2.7/bioc/vignettes/Category/inst/doc/Category.pdf

Best,

Jim


>
> 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.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues