[BioC] P-values for tissue specific genes
Pascal_G at web.de
Tue Jul 15 09:42:51 CEST 2008
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?
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