Hi all, I have six samples with the following design ID Sample Type C1 A Control C2 A Treated C3 B Control C4 B Treated C5 C Control C6 C Treated A, B, and C are three patients Would a paired t-test work better than one-way ANOVA here? Do I need more replicates? thanks for your help Yogi

Hi Yogi, Yogi Sundaravadanam wrote: > Hi all, > > I have six samples with the following design > ID Sample Type C1 A Control C2 A Treated > C3 B Control C4 B Treated > C5 C Control > C6 C Treated > > A, B, and C are three patients > > > Would a paired t-test work better than one-way ANOVA here? Do I need > more replicates? You definitely want to account for the intra-patient dependence structure somehow. One way would be to do a paired t-test. The other way would be to do a linear mixed model-ish thing using duplicateCorrelation() to capture the intra-patient correlation. There have been numerous posts about the latter, and if I am not mistaken there is an example in the Limma User's Guide as well. Best, Jim > > thanks for your help > Yogi > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826