Question: Compare in cont.matrix part
1
7 months ago by

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)

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

microarray R • 168 views
modified 7 months ago by Gordon Smyth36k • written 7 months ago by morteza.hadizade10
1
7 months ago by
United States
James W. MacDonald49k wrote:

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?

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.

1
7 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

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.