In the package affycoretools, how does the function limma2annaffy determine which fold change to output in the case of multiple contrasts? In topTable, one can specify the coefficient, but I don't see that this is the case with limma2annaffy. Thanks, Mark W Kimpel Indiana University School of Medicine

Hi Mark, Kimpel, Mark William wrote: > In the package affycoretools, how does the function limma2annaffy > determine which fold change to output in the case of multiple contrasts? > In topTable, one can specify the coefficient, but I don't see that this > is the case with limma2annaffy. In limma2annaffy, one of the arguments you supply is the contrasts matrix. This is used to extract the fold change, t-statistic, p-value, and expression values for the resulting HTML or text table. The default is to output results for _all_ contrasts, so you don't explicitly specify the coefficient. HTH, Jim > > > Thanks, > > Mark W Kimpel > Indiana University School of Medicine > > _______________________________________________ > 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, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.