Hi,
I am using edgeR post kallisto to look for DGE.
I have RNAseq samples from 4 different tissue types and my design currently looks like this:
> head(design)
(Intercept) D.new$samples[, 1]CA Endothelium
1 1 1
2 1 1
3 1 1
4 1 1
5 1 1
6 1 1
D.new$samples[, 1]CA Smooth Muscle D.new$samples[, 1]Coronary Artery
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
...
attr(,"assign")
[1] 0 1 1 1
attr(,"contrasts")
attr(,"contrasts")$`D.new$samples[, 1]`
[1] "contr.treatment"
So my four tissue types are Aorta (intercept), CA Endothelium, CA Smooth Muscle and Coronary Artery.
As I understand I can compare gene expression between any tissue using:
lrt.ECvsAo<-glmLRT(fit.new, contrast=c(1,-1,0,0))
If I use this contrast
lrt.ECvsAll<-glmLRT(fit.new, contrast=c(1,-1,1,1))
am I asking for DGE between the second column (CA Endothelium) and EITHER other tissue?
I'd like to find genes that are differentially expressed between CA Endothelium and ALL Aorta, CA Smooth Muscle and Coronary Artery.
Is this doable?
Many thanks
I am using edgeR post kallisto to look for DGE.
I have RNAseq samples from 4 different tissue types and my design currently looks like this:
> head(design)
(Intercept) D.new$samples[, 1]CA Endothelium
1 1 1
2 1 1
3 1 1
4 1 1
5 1 1
6 1 1
D.new$samples[, 1]CA Smooth Muscle D.new$samples[, 1]Coronary Artery
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
...
attr(,"assign")
[1] 0 1 1 1
attr(,"contrasts")
attr(,"contrasts")$`D.new$samples[, 1]`
[1] "contr.treatment"
So my four tissue types are Aorta (intercept), CA Endothelium, CA Smooth Muscle and Coronary Artery.
As I understand I can compare gene expression between any tissue using:
lrt.ECvsAo<-glmLRT(fit.new, contrast=c(1,-1,0,0))
If I use this contrast
lrt.ECvsAll<-glmLRT(fit.new, contrast=c(1,-1,1,1))
am I asking for DGE between the second column (CA Endothelium) and EITHER other tissue?
I'd like to find genes that are differentially expressed between CA Endothelium and ALL Aorta, CA Smooth Muscle and Coronary Artery.
Is this doable?
Many thanks
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