Limma/edgeR Design matrix for gender effect
Hi,
I'm trying to do an RNA-seq analysis using edgeR and want to negate the contribution of gender in my samples. Control (3 Male, 1 Female), Treated (4 Male, 1 Female). I want to find DE genes as a result of treatment. I wanted to know if my design file and contrast.matrix file makes sense?
group$group
1 WT_F
2 WT_F
3 WT_M
4 WT_F
5 RX_F
6 RX_F
7 RX_M
8 RX_F
9 RX_F
design file:
groupRX_F groupRX_M groupWT_F groupWT_M
1 0 0 1 0
2 0 0 1 0
3 0 0 0 1
4 0 0 1 0
5 1 0 0 0
6 1 0 0 0
7 0 1 0 0
8 1 0 0 0
9 1 0 0 0
attr(,"assign")
[1] 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
contrast.matrix:
Contrasts
Levels RXvsWT
groupRX_F 1
groupRX_M 1
groupWT_F -1
groupWT_M -1
1 answer
Log in to answer this question.
More posts like this
-
Issue when using design matrix taking batch effect into account - EdgeR RNA-seq
written by maxime •
-
edgeR design matrix error not of full rank
written by intropin •
-
error in R
written by Bioinformatics1 •
-
Problems in differential expression analysis with edgeR
written by thancy •
-
What is the right design matrix in a Microarray data analysis?
written by Paul Paodumai •
-
Extracting data from edgeR R package
written by Sara
-
problem with create design in edgR
written by weiyanjia2008 •
-
edgeR batch effect
written by NielQC •
-
full rank designe matrix?
written by star
-
Differential Expression Analysis In Limma For One Factor After Adjusting For A Covariate
written by aditi.qamra
Did you check by PCA or MDS if there is some evidence for this batch effect (I guess not simply because variation between human individuals is probably way more confounded by factors such as life style, health status, diet, consumption of drugs (medical, alcohol, cigarets) etc. = did the females cluster away from the bulk of the males?
Yes, PCA showed that the males samples were away from the rest of the group.