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)
Thank you for your answer, but LogFC is important in our results final (up and down-regulated genes), if I remove the single quotes, LogFC is removed from the analysis result. So I have to compare two groups in cont.matrix.