Question: Compare in cont.matrix part
1
gravatar for morteza.hadizade
7 months 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)

microarray R • 168 views
ADD COMMENTlink modified 7 months ago by Gordon Smyth36k • written 7 months ago by morteza.hadizade10
Answer: Compare in cont.matrix part
1
gravatar for James W. MacDonald
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?

ADD COMMENTlink written 7 months ago by James W. MacDonald49k

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 7 months ago by morteza.hadizade10
Answer: Compare in cont.matrix part
1
gravatar for Gordon Smyth
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.

 

ADD COMMENTlink modified 7 months ago • written 7 months ago by Gordon Smyth36k

Thank you for your help

ADD REPLYlink written 7 months ago by morteza.hadizade10
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