[BioC] Fisher-test
Naomi Altman
naomi at stat.psu.edu
Sat Aug 7 05:41:26 CEST 2010
You are not using the Fisher test correctly. The entries in the
table should be counts.
--Naomi
At 05:00 PM 8/3/2010, Noe Andor wrote:
>Hello,
>
>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,
>
>Noemi
>
>
> [[alternative HTML version deleted]]
>
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Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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