[BioC] EdgeR design question?

[Gordon K Smyth]

Dear Joseph,

You have not fitted the right model.  You need

    ~ Genotype + Genotype:Age

instead of

    ~ Age + Age:Genotype

You can follow the section 3.3.2 in the edgeR User's Guide.

Best wishes
Gordon

> Date: Sat, 11 Jan 2014 12:36:07 -0800 (PST)
> From: joseph <jdsandjd at yahoo.com>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] EdgeR design question?
>
> 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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