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joseph
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330
@joseph-1270
Last seen 10.2 years ago
Hi
I am using edgeR to analyse an RNA-seq experiment with two factors,
age (Young, Old) and genotype (Wt, Mutant).
> targets
Age Genotype
Sample1 Young Wt
Sample2 Young Wt
Sample3 Young Wt
Sample4 Young Mutant
Sample5 Young Mutant
Sample6 Young Mutant
Sample7 Old Wt
Sample8 Old Wt
Sample9 Old Wt
Sample10 Old Mutant
Sample11 Old Mutant
Sample12 Old Mutant
I know from previous experiments that the age effect is different
between Wt and Mutant genotypes.
I would like to find:
1. genes that change with age in Wt.
2. genes that change with age in Mutant.
3. genes that change with age differently between the genotypes
(interaction).
Can the following approach answer these questions?
targets$Age <- relevel(targets$Age, ref="Young")
targets$Genotype <- relevel(targets$Genotype, ref="Wt")
design1 <- model.matrix(~Age + Age:Genotype, data=targets)
> design1
(Intercept) AgeOld AgeYoung:GenotypeMutant
AgeOld:GenotypeMutant
Sample1 1 0 0
0
Sample2 1 0 0
0
Sample3 1 0 0
0
Sample4 1 0 1
0
Sample5 1 0 1
0
Sample6 1 0 1
0
Sample7 1 1 0
0
Sample8 1 1 0
0
Sample9 1 1 0
0
Sample10 1 1 0
1
Sample11 1 1 0
1
Sample12 1 1 0
1
attr(,"assign")
[1] 0 1 2 2
attr(,"contrasts")
attr(,"contrasts")$Age
[1] "contr.treatment"
attr(,"contrasts")$Genotype
[1] "contr.treatment"
I think coef=4 in design1 represents the genes that change with age in
Mutant; but I don't know what coefficient represents the genes that
change with age in Wt.
design2 <- model.matrix(~Age*Genotype, data=targets)
> design2
(Intercept) AgeOld GenotypeMutant AgeOld:GenotypeMutant
Sample1 1 0 0 0
Sample2 1 0 0 0
Sample3 1 0 0 0
Sample4 1 0 1 0
Sample5 1 0 1 0
Sample6 1 0 1 0
Sample7 1 1 0 0
Sample8 1 1 0 0
Sample9 1 1 0 0
Sample10 1 1 1 1
Sample11 1 1 1 1
Sample12 1 1 1 1
attr(,"assign")
[1] 0 1 2 3
attr(,"contrasts")
attr(,"contrasts")$Age
[1] "contr.treatment"
attr(,"contrasts")$Genotype
[1] "contr.treatment"
coef=4 in design2 represents the interaction of age and genotype.
Thank you for your help
Joseph
> sessionInfo()
R version 3.0.2 Patched (2013-10-28 r64119)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.4.2 limma_3.18.7
loaded via a namespace (and not attached):
[1] tools_3.0.2
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