[BioC] vennDiagram Statistics Advice

[Wolfgang Huber]

Dear Noah

a first, immediate answer is to look at
  ? fisher.test

Some light reading on its background can be found here: 
http://en.wikipedia.org/wiki/Fisher%27s_exact_test
and see e.g. Agresti's excellent book 'Categorial Data Analysis' for 
something more substantial.

The second, more conceptual and perhaps more useful answer is to use 
heatmaps and clustering of the expression profiles to show the desired 
similarity relationships between the 4 expression profiles.

Simply using Euclidean distance, say on the subset of genes that is the 
union of all differentially expressed genes, on the fold changes should 
be a good start.

	Best wishes
	Wolfgang


Noah Dowell scripsit 27/04/10 00:37:
> Dear All,
> 
> I have used the excellent limma package to analyze my 2-color Agilent Yeast microarray data and have determined the differentially expressed genes (as compared to wild-type expression) in four independent experiments.  I am showing the summary of my results below:
> 
>> results <- decideTests(fit2, method="global")
> 
>> summary(results)
> 
> # mutant1 mutant2 mutant3  deletionstrain
> #-1       147       126        40        252
> # 0       5924      6033      6171       5600
> # 1        185        97        45        404
> 
> 
> The three mutant experiments represent expression data from cells expressing different point mutants in the gene that is deleted in the expression strain.  The point mutation in Mutant3 is a control that should not affect the protein's function given our current knowledge of how the protein works therefore the relatively small number of genes differentially expressed as compared to wild-type is consistent with our using that strain as a "control."
> 
> Mutants1 and 2 are similar in their biological defects.  They are also hypomorphic alleles as compared to the complete deletion strain so the smaller number of differentially expressed genes is again consistent with our working model.
> 
> I have created vennDiagrams of these four experiments to look at the overlap of differential expression between experiments.
> 
> My question is if there is a test I can run on the vennDiagrams (or simply on the overlapping gene lists) to show that there is significantly more overlap between mutant 1 or mutant 2 and the deletion strain when compared to mutant 3?
> 
> Thank you for your time and input!
> 
> Noah
> 
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber