[BioC] P-values for tissue specific genes
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Tue Jul 15 19:45:44 CEST 2008
On Jul 15, 2008, at 12:42 AM, Pascal Gellert wrote:
> 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?
Whether or not this contrast matrix makes sense depends on your design
Given your p-values I would guess you are doing something wrong, but I
have no idea what. There could also be some problems with your data
but again it is hard to tell you what is wrong. Take a look at the raw
data for some of the genes with a p-value of zero, perhaps you can
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