[BioC] fisher-test

Noemi Andor Noemi.Andor at campus.lmu.de
Wed Aug 4 00:23:12 CEST 2010


I have a question regarding fiher-test & differential gene expression. I usually use ttest to see which genes are differential expressed between two sample-types. I thought of using fisher test for the first time, to see if results are comparable, yet I'm not shure if I applyed it correctly. I made a 2x2 contingency table for each gene, like:

   Notch1-Normal    Notch1-Tumor
up            x                        x2
down        y                        y2

x = Sum of all foldchanges from normal samples (min foldchange = 1.5)
y = Sum of all foldchanges from normal samples (max foldchange = 0.5)

...analogue for tumor samples.

Then I applyed Fisher test:

tab<-c(x, x2, y, y2)
fisher.test(tab, alternative="two.sided")

Yet I got no significant results (as compared to the t-test results, which harbor some good hits) - so I assume I did'n built the table the right way.
I would be greatfull for an example, especially regarding that contingency table.

best regards,


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