Hi everyone,

In the cont.matrix, can I compare each individual group separately (Not altogether)?

Thanks you very much for your attention.

cont.matrix<- makeContrasts (TGFbeta-Control, levels=design)

or

cont.matrix<- makeContrasts (SSc – Control, levels=design)

instead

cont.matrix<- makeContrasts (c('TGFbeta-Control', 'SSc - Control'), levels=design)

It's not clear what you are asking. The last example, if you remove the single quotes, should do what you seem to want. Did you not try that?

Why not either

cont.matrix <- makeContrasts(TGFbeta-Control, SSc–Control, levels=design)

or

cont.matrix <- makeContrasts(contrasts=c('TGFbeta-Control','SSc-Control'), levels=design)

It seems so me that reading help("makeContrasts") would answer your questions. There are usage examples at the bottom of the help page.