Dear i am facing a problem during anova in microarray. basically i have 4 different groups with more than 5 repitions. during SAM analysis b/w two groups i got fold induction but for more than two groups i have to perfom anova. and anova could not tell me about fold induction. can any one guide me to how get fold induction value from anova Regards Waqar Ahmad Research Officer CEMB Lahore Pakistan

Hello Waqar, I think we'll need a bit more details from you in order to help you properly. You don't get the fold induction directly from anova, but you can easily calculate it yourself. How to do this depends on what kind of data you have though. Two-colour microarrays? Single-colour arrays (like affymetrix)? Either way, the fold induction is the log2 ratio, so for example log2(red channel/green channel) or log2(sample/control). Again, the exact command(s) to use depends on what kind of object you have your data in. ExpressionSet? Something else? Another approach would be to use the package limma, which will report the log ratios along with adjusted p-values etc. Regards \Heidi > Dear > > i am facing a problem during anova in microarray. > basically i have 4 different groups with more than 5 repitions. > during SAM analysis b/w two groups i got fold induction but for more than > two groups i have to perfom anova. and anova could not tell me about fold > induction. > can any one guide me to how get fold induction value from anova > > Regards > Waqar Ahmad > Research Officer > CEMB > Lahore > Pakistan > > _______________________________________________ > 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