Dear Bioconductors, In analyse of DNA microarray using LIMMA: for example you have a contrast matrix like follow: ---makeContrasts(B-A,C-B,levels=c("A","B","C")) then it is fitted to linear model and eBayes function is used to summarize the statistics. Finally log odds is used to rank the differential genes. I am wondering is the log odds rank the genes which express different between condition B and A (B-A), or C and B(C-B), or different in both conditions, or in either conditions? how to explain it? Expecting your reply! Regards, Yanju

Hi Yanju, yanju at liacs.nl wrote: > Dear Bioconductors, > > In analyse of DNA microarray using LIMMA: for example you have a contrast > matrix like follow: > ---makeContrasts(B-A,C-B,levels=c("A","B","C")) > then it is fitted to linear model and eBayes function is used to summarize > the statistics. > Finally log odds is used to rank the differential genes. > > I am wondering is the log odds rank the genes which express different > between condition B and A (B-A), or C and B(C-B), or different in both > conditions, or in either conditions? how to explain it? The log odds rank the genes differently for each individual contrast. If you type topTable(<marraylm_object>, coef = 1), you will get the top genes in the first contrast, and if you type topTable(<marraylm_object>, coef = 2), you get the top genes in the second contrast. HTH, Jim > > Expecting your reply! > > Regards, > Yanju > > _______________________________________________ > 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 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.