Entering edit mode
6.6 years ago
Sanches
•
0
Hi all,
I am using Limma for the first time to analyze my two-color microarray data. So, I would like to know the best way to proceed to create my Targets file. My experiment has the following technical replicates:
CY3 CY5
1. gene of interest control
2. gene of interest control
3. control gene of interest
4. control gene of interest
5. gene of interest (treated) control (treated)
6. gene of interest (treated) control (treated)
7. control (treated) gene of interest(treated)
. 1=2 / 3=4 / 5=6
My question is: how can I proceed in this part below?
targets <- cbind(Cy3=c("Gene of interest","Gene of interest", "Control", "Control", "Gene of interest_Treatment", "Gene of interest_Treatment", "Control_Treatment"), Cy5=c("Control", "Control", "Gene of interest", "Gene of interest", "Control_Treatment", "Control_Treatment", "Gene of interest_Treatment"))
rownames(targets) <- paste("Array",1:7)
parameters <- cbind(C=c(-1,-1, 0, 0, 1, 1, 2), T=c(0, 0, -1, -1, 2 , 2, 1))
rownames(parameters) <- c("Reference","Control","Treatment") **# What is the right way to write this part?**
modelMatrix(targets, parameters)
modelMatrix(targets, ref="Reference")
design<- model.matrix(targets, parameters)
Thanks in advance
cheers,
Paulo