Dear all, My current analysis revolves around various groups and their subgroups, which is why I would like to know how I can pool two or more subgroups in a contrast matrix. As an example, let us assume I have 4 main groups (A, B, C and D), of which one can be subdivided into 3 subgroups (B1, B2 and B3), hence groups = c("A","B1","B2","B3","C","D") Now, I would like to compare the combined/pooled group B (consisting of B1, B2 and B3) against all other groups, B vs A, B vs C, B vs D. So my question is: how do I formalize that with makeContrasts() for an analysis with limma? If it would be different matrices, I would just use cbind(), however I am not sure whether B1+B2+B3 does the same thing in makeContrasts(). Thank you in advance and best regards

Hi Ren?, On 1/23/2013 4:14 AM, Ren? wrote: > Dear all, > > My current analysis revolves around various groups and their > subgroups, which is why I would like to know how I can pool two or > more subgroups in a contrast matrix. > As an example, let us assume I have 4 main groups (A, B, C and D), of > which one can be subdivided into 3 subgroups (B1, B2 and B3), hence > > groups = c("A","B1","B2","B3","C","D") > > Now, I would like to compare the combined/pooled group B (consisting > of B1, B2 and B3) against all other groups, > > B vs A, B vs C, B vs D. > > So my question is: how do I formalize that with makeContrasts() for an > analysis with limma? > If it would be different matrices, I would just use cbind(), however I > am not sure whether B1+B2+B3 does the same thing in makeContrasts(). You are almost there. Note that you want the mean of the three groups, not the sum. So makeContrasts((B1 + B2 + B3)/3 - A) will e.g., do the comparison of B vs A. Best, Jim > > Thank you in advance and best regards > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099