Question: Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
gravatar for jth
5.6 years ago by
jth190 wrote:

I would like to find out differentially expressed genes in 4 different groups; however, each group has triplicates. So, what is the correct way to follow in this scenario in order to compare the groups between themselves? I guess i can do it if they were single, but being in triplicate confuses me a bit.

Data is from Illumina HumanHT-12 v4 Expression BeadChip, i exported from GenomeStudio v2011.

Thanks a lot!

R limma illumina microarray • 3.1k views
ADD COMMENTlink modified 5.6 years ago by seidel6.8k • written 5.6 years ago by jth190
gravatar for seidel
5.6 years ago by
United States
seidel6.8k wrote:

Take a look at Chapter 7 (Linear Models Overview) of the limma users guide. It has some good examples. To compare 4 groups consisting of triplicate samples you would do something like the following:

    design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2,3,3,3,4,4,4)))
    colnames(design) <- c("group1", "group2", "group3", "group4")
    # call lmFit on your data
    fit <- lmFit(yourdata, design)

    # create you comparisons of interest        
    contrast.matrix <- makeContrasts(group2-group1, group3-group2, group3-group1, group4-group1, group4-group3, group4-group2, levels=design)

    fit2 <-, contrast.matrix)
    fit2 <- eBayes(fit2)
    # fit 2 now contains all your comparisons
ADD COMMENTlink written 5.6 years ago by seidel6.8k

Thanks a lot for the answer!

ADD REPLYlink written 5.6 years ago by jth190
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1785 users visited in the last hour