[BioC] fisher exact test pairwise comparisons

[Ann Loraine]

Hi,

I'm also interested in this question.

How would you recommend handling replicates?

For example, if you had counts for each of three control samples and
each of three treatments, would it make sense to run "sage.test" for
every combination,  get a p value for each test, and then combine them
somehow?

-Ann

On Wed, Mar 7, 2012 at 9:30 AM, Naomi Altman <naomi at stat.psu.edu> wrote:
> Look at package sagenhaft, function sage.test.
>
> --Naomi
>
> At 04:40 AM 3/7/2012, Alyaa Mahmoud wrote:
>>
>> Dear Group
>>
>> I would like to perform a pairwise comparisons using fisher exact test for
>> 5 samples (columns) and 3835 genes (rows). Is there a way I can do the
>> pairwise comparison at one time ?
>>
>> I would highly appreciate any help
>> Thanks a lot
>>
>> yours,
>> Alyaa Mahmoud
>>
>> --
>> Alyaa Mahmoud
>>
>> "Love all, trust a few, do wrong to none"- Shakespeare
>>
>>        [[alternative HTML version deleted]]
>>
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>
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