Question: Limma design matrix
0
gravatar for R
17 months ago by
R40
Germany
R40 wrote:

I have data with Treated and Control and three time-groups within each.
I want to compare across the time-groups for Treated vs Control.
How do I set up my desing matrix?

    groupTC = c("C","C","C","C","C","C","T","T","T")

    groupTC_Time = c("Early","Early","Mid,"Mid","Late,"Late","Early","Early","Mid,"Mid","Late,"Late",)

I want to compare Early vs Late and Early vs Mid for Treated vs Control?.

 

 

limma design matrix • 265 views
ADD COMMENTlink modified 17 months ago by Gordon Smyth38k • written 17 months ago by R40
Answer: Limma design matrix
0
gravatar for James W. MacDonald
17 months ago by
United States
James W. MacDonald51k wrote:

Have you read the limma User's Guide? Section 9.6 specifically deals with timecourse experiments.

ADD COMMENTlink written 17 months ago by James W. MacDonald51k
Answer: Limma design matrix
0
gravatar for Gordon Smyth
17 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

I usually advise people to setup the design matrix in the standard way, as in Section 9.5.2 of the User's Guide:

Group <- paste(GroupTC, GroupTC_Time, sep=".")
Group <- factor(Group)
design <- model.matrix(~0+Group)
colnames(design) <- levels(Group)

Then use makeContrasts() to make whatever comparisons you like.

ADD COMMENTlink written 17 months ago by Gordon Smyth38k
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