[BioC] P-values for tissue specific genes
sean.maceach at gmail.com
Tue Jul 15 14:34:30 CEST 2008
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
You can have a look at this paper to see if it is of any help:
Genet. Sel. Evol. 38 (2006) 321-341
On 7/15/08 3:42 AM, "Pascal Gellert" <Pascal_G at web.de> 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
> Please help
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