[BioC] edgeR: design matrix for different condition

[Gordon K Smyth]

Dear KJ Lim,

I don't quite understand your question, because you seem to be asking for 
something that isn't a test for differential expression, which is what 
edgeR does.  You question "I would like to learn the genes are express in 
treeHS but not treeLS and vice versa" seems to be about absolute 
expression levels.  edgeR doesn't test for genes that are not expressed in 
particular conditions.

I'll refer you to the limma section on interaction models in case that 
helps, see Section 8.5 of:

http://bioconductor.org/packages/2.11/bioc/vignettes/limma/inst/doc/usersguide.pdf

Setting up a design matrix is the same for edgeR as it is for limma.

Best wishes
Gordon

> Date: Tue, 24 Jul 2012 17:12:00 +0300
> From: KJ Lim <jinkeanlim at gmail.com>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] edgeR: design matrix for different condition
>
> Dear the edgeR community,
>
> Good day.
>
> I'm analyzing my RNA-Seq experiment with edgeR. My study has 2
> different genotypes (treeHS, treeLS) and time of treatment (0H, 3H,
> 24H, 96H).
>
> I first assumed that the treatment effect will be the same for each
> genotype and I have the design matrix as:
>
>  design <- model.matrix(~tree+treat)
>
>> design
>   (Intercept)  treat03H  treat24H  treat96H  treeLS
> 1             1        0        0        0      0
> 2             1        0        0        0      0
> 3             1        1        0        0      0
> 4             1        1        0        0      0
> 5             1        0        1        0      0
> 6             1        0        1        0      0
> 7             1        0        0        1      0
> 8             1        0        0        1      0
> 9             1        0        0        0      1
> 10           1        0        0        0      1
> 11           1        1        0        0      1
> 12           1        1        0        0      1
> 13           1        0        1        0      1
> 14           1        0        1        0      1
> 15           1        0        0        1      1
> 16           1        0        0        1      1
>
> I used coef=4 to test for the differential expressions between treeHS
> and treeLS within the time of treatment, coef=3 to learn the
> differential expressions in 2 genotypes at time of treatment 96H.
>
> ** I would like to learn the genes are express in treeHS but not
> treeLS and vice versa at certain time of treatment let's say 24H or
> across the whole time of treatment, should I have the design matrix as
> below or more steps I need to do?
>
>  design <- model.matrix(~tree*treat)
>
> Kindly please light me on this. I appreciate very much for your help and time.
>
> Have a nice day.
>
> Best regards,
> KJ Lim
>

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