[BioC] P-values for tissue specific genes

[Sean MacEachern]

Hi Pascal,

You could always look at modifying a chi-square test so that a given gene is
classified as being tissue specific if it's value in one tissue is over the
expected value? 

You can have a look at this paper to see if it is of any help:
Genet. Sel. Evol. 38 (2006) 321-341
 

Cheers,

Sean


On 7/15/08 3:42 AM, "Pascal Gellert" <Pascal_G at web.de> wrote:

> Hello,
> 
> unfortunately I have I big problem I can't solve.
> 
> I have to analyze if a gene is tissue specific. For example for the gene xyz I
> have following expression values:
> 
> Heart           Liver              Brain        ....several others
> 8.998497   10.013561   12.277407
> 9.743556   10.137574   11.033957
> 
> For every tissue I have two values from two different experiments.
> 
> Now I want to test if Heart is significant higher than Liver and Brain, or
> Liver is significant higher than Heart an Brain, ...
> 
> I read about the pairwise.t.test, but I dont't want to test Heart against
> Liver and Heart against Brain, ...
> 
> Is there any possibility to do that? ANOVA? Duncan? Constrasts?
> 
> When I set up a contrasts matrix like
> 
>           Heart        Liver           Brain
> C1        1             -1/2           -1/2
> C2       -1/2            1             -1/2
> C3       -1/2         -1/2              1
> 
> to get tissue specific genes, some p-values are exact 0 (even I corrected with
> holm). This can't be correct? Are only degree of freedoms times contrasts
> allowed?
> 
> 
> Please help 
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