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Question: Compare in cont.matrix part
1
gravatar for morteza.hadizade
6 days ago by
morteza.hadizade10 wrote:

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)

ADD COMMENTlink modified 5 days ago by Gordon Smyth34k • written 6 days ago by morteza.hadizade10
1
gravatar for James W. MacDonald
6 days ago by
United States
James W. MacDonald47k 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?

ADD COMMENTlink written 6 days ago by James W. MacDonald47k

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.

ADD REPLYlink written 5 days ago by morteza.hadizade10
1
gravatar for Gordon Smyth
5 days ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k 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.

 

ADD COMMENTlink modified 5 days ago • written 5 days ago by Gordon Smyth34k

Thank you for your help

ADD REPLYlink written 5 days ago by morteza.hadizade10
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