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]]

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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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