R help - Oct 2010 - Fisher exact test?

Hi All,

My apologies if this is a totally newbie question. 

I want to calculate the probability that a particular set of genes is picked 
repeatedly for 3 samplings. For example, if from a total of 'N' genes, I
pick
'A' number of genes in the first pick, 'B' number of genes in
the second pick,
and 'C' number of genes in the third pick, I would want to calculate
p(n) where
n = (A intersection B intersection C).

Would fisher exact test be the correct method to evaluate the probability? And 
if so how can I frame the 3x3 (?) contingency table? I can find numerous 
examples of 2x2 tables, but none for 3x3. Any guidance would be appreciated.

many thanks.


      
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To find the probability directly, you'll need to clearly state how you are
sampling.  Are you sampling with replacement? (Draw then put back.)  Or are
you sampling without replacement? (Draw.  Draw from the remaining.  Draw
from the remaining.)

Also, of the N genes, do you know how many are of the particular set?
How many genes do you draw each try?

Does order matter to you?  In other words is (A=5, B=0, C=23) equivalent to
(A=0,B=5,C=23)?

-tgs

On Mon, Oct 4, 2010 at 10:13 AM, James Nead <james_nead@yahoo.com> wrote:
> Hi All,
>
> My apologies if this is a totally newbie question.
>
> I want to calculate the probability that a particular set of genes is
> picked
> repeatedly for 3 samplings. For example, if from a total of 'N'
genes, I
> pick
> 'A' number of genes in the first pick, 'B' number of genes
in the second
> pick,
> and 'C' number of genes in the third pick, I would want to
calculate p(n)
> where
> n = (A intersection B intersection C).
>
> Would fisher exact test be the correct method to evaluate the probability?
> And
> if so how can I frame the 3x3 (?) contingency table? I can find numerous
> examples of 2x2 tables, but none for 3x3. Any guidance would be
> appreciated.
>
> many thanks.
>
>
>
>        [[alternative HTML version deleted]]
>
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> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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