Question: Limma Design matrix for time series+treatment+batch effect
0
gravatar for senthil.duraikannukailasam
23 days ago by

dear all, I'm trying to get a DEG analysis of a microarray data.

I have 9 placebo and 9 treated mouse samples. The

3 replicates for each condition factors: 1. TimeOfTreatment <- "2days", " 7days", "12days" 2. TreatmentType <- "placebo" , "drug" 3. BatchID <- "001" , "002"

  TimeOfTreatment <- rep(c("2","4","6","2","4","6","2","4","6"),2)
  TreatmentType <- rep(c("placebo","drug"),9)
  BatchID  <- rep(c("1","1","2","1","1","1","2","1","1"),2)
  groupS <- paste(TimeOfTreatment,TreatmentType,sep= "_")

  model.matrix(~ 0 + groupS + Batch)

Now, I'm not sure how to get the contrast matrix!
For say , 1. I wanted to compare the DGE between all Treated and untreated samples. 2. Between Drug Treated 6th day with Drug Treated 4th day. 3. Between Drug Treated 4th day with Drug Treated 2nd day.

ADD COMMENTlink modified 19 days ago by Aaron Lun24k • written 23 days ago by senthil.duraikannukailasam0
Answer: Limma Design matrix for time series+treatment+batch effect
2
gravatar for Aaron Lun
19 days ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Just use makeContrasts. You will have to fix your names so that they are syntactically valid, though.

I wanted to compare the DGE between all Treated and untreated samples.

Compare averages of the groupS levels, e.g., (A1 + A2 + A3)/3 - (B1 + B2 + B3)/3.

Between Drug Treated 6th day with Drug Treated 4th day. 3. Between Drug Treated 4th day with Drug Treated 2nd day.

Compare the relevant levels of groupS, e.g., Drug4 - Drug2, and so on.

ADD COMMENTlink modified 19 days ago • written 19 days ago by Aaron Lun24k
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