Hi James, Thanks a lot for clarifying, now I can continue with my analysis. Best regards, Ren? > 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 >