Question: Problem with the design matrix in limma
gravatar for ap-91
21 months ago by
ap-910 wrote:


I'm Andrea and i'm a student. Currently, I'm work on phosphoproteomic data collected in an excel file. In particular, i have in each row the expression levels of gene for mutant and wild-type condition, 3 replicas for each condition (six columns: M1 M2 M3 WT1 WT2 WT3 - exe: gene1: M1 M2 M3 WT1 WT2 WT3). I have a question on the design matrix because i'm not sure i did well. This is my design matrix:

## Design Matrix 
samples = factor(c(rep("M", each = 3), rep("WT", each = 3)))
design = model.matrix(~ 0+samples)
colnames(design) = levels(samples)
rownames(design) = colnames(Data)

> design
       M WT
M1   1  0
M2   1  0
M3   1  0
WT1 0  1
WT2 0  1
WT3 0  1
[1] 1 1
[1] "contr.treatment"

Is it correct? Please, someone could help me? Thanks, Andrea.

R • 592 views
ADD COMMENTlink modified 21 months ago by ATpoint39k • written 21 months ago by ap-910

Please use the formatting bar and especially the code option (10101) to highlight code and data examples. I've done the changes this time.

ADD REPLYlink written 21 months ago by ATpoint39k
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: 976 users visited in the last hour