Question: LIMMA 2x2 with time
gravatar for Ahdee
22 months ago by
United States
Ahdee40 wrote:

Hi can someone take a look at this and see if my design is correct?  What I'm trying to achieve is similar to a 2-way ANOVA main effect and interactions with LIMMA.  

I would like to look at the main effect of gene, time and interaction as well as comparison of gene regardless of time. Sorry if this has been asked before, but  I was hoping to get some confirmation.  


ds <- read.table(header = TRUE, text =
                 "id gene time
                   1 gfp t24
                  2 ko   t24
                  3 gfp t75
                  4 ko t75

ft <- paste(ds$time,ds$gene,sep=".")

ft <- factor(ft)
design2 <- model.matrix(~0+ft)
colnames(design2) <- levels(ft)

cont.matrix <- makeContrasts(
  gene.main = "(t24.ko + t75.ko)/2 - (t24.gfp + t75.gfp)/2", 
  time.main = "(t75.gfp + t75.ko)  /2  - (  t24.gfp +  t24.ko) /2 ",
  Interaction="(t24.ko - t75.ko) - (t24.gfp - t75.gfp)",
  gfp.vs.ko = " (t24.ko + t75.ko) - (t24.gfp + t75.gfp) "





limma limma design matrix • 304 views
ADD COMMENTlink modified 22 months ago by James W. MacDonald49k • written 22 months ago by Ahdee40
Answer: LIMMA 2x2 with time
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald49k wrote:

You need to divide by two for the last contrast as well, but otherwise seems ok to me. Plus I don't think you want to use quotes

ADD COMMENTlink written 22 months ago by James W. MacDonald49k

Thanks James! After reading over you comment I just realized that what I want is indeed the same as the main effect for gene.main.  great thanks again. 


ADD REPLYlink written 22 months ago by Ahdee40
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