[BioC] P-values for tissue specific genes

[Pascal Gellert]

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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