[R] Fisher test for a more than two group of genes‏

[David Winsemius]

On Aug 28, 2013, at 11:53 AM, Gabriel Wajnberg wrote:
> 
> Good Afternoon,
> My name is Gabriel, I'm doing an analysis if there is increase or decrease in dependence on the mutated genes, using 3 or more genes using the fisher exact test.I performed with success an analysis for two genes using fisher.test( ). example of the 2x2 contigency table:

Edited original table:

>               Gene A mutated | Gene A normal
> Gene B mutated| 26           |        12
> ------------------------------------------------
> Gene B normal |  10          |        50
> 
> Now I'm wondering how can I perform the analysis for 3 genes (and construct the contigency table), as follows: Gene A mutated, Gene A normal, Gene B mutated, Gene B normal, Gene C mutated and Gene C normal. How do I perform a fisher test using fisher.test( ) function using this data (3x3 contigency table)?Can someone help me ?
> 		 	   		   		 	   		  
> 	[[alternative HTML version deleted]]

I'm guessing you failed to read the Posting Guide where you are asked not to post in HTML format. I also don't understand what problems youa re having when you use fisr.test with a 3x3 table. Its help page says it acna handle a 2 dimnensional contingency table.

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David Winsemius
Alameda, CA, USA