Search
Question: Compare in cont.matrix part
1
gravatar for morteza.hadizade
10 weeks 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 9 weeks ago by Gordon Smyth35k • written 10 weeks ago by morteza.hadizade10
1
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald48k 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 9 weeks ago by James W. MacDonald48k

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 9 weeks ago by morteza.hadizade10
1
gravatar for Gordon Smyth
9 weeks ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k 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 9 weeks ago • written 9 weeks ago by Gordon Smyth35k

Thank you for your help

ADD REPLYlink written 9 weeks ago by morteza.hadizade10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 200 users visited in the last hour