[Bioc-sig-seq] interaction factor in edgeR

[Gordon K Smyth]

Dear Fernando,

> Date: Tue, 10 May 2011 13:40:23 -0500
> From: "Biase, Fernando" <biase at illinois.edu>
> To: "bioc-sig-sequencing at r-project.org"
> 	<bioc-sig-sequencing at r-project.org>
> Subject: [Bioc-sig-seq] interaction factor in edgeR
>
> Dear list users,
>
> I am not a statistician, so pardon my ignorance.
>
> When using edgeR package to analyse RNA-seq data the number of 
> differential expressed genes vary depending on whether I use an 
> interaction factor in the design. Can anyone suggest why does it happen?

Well, you fit a different model, and test a different hypothesis, so the 
results change.  No doubt the residual dispersion has changed as well. 
Wouldn't you be worried if the results didn't change?

> Example:
>
> if I use:
> design <- model.matrix(~ a + b  , data=targets)
>
> I have:
> summary(decideTests_eset_b_tmm)
>   [,1]
> -1  2855
> 0  12346
> 1   4928
>
> if I use:
> design <- model.matrix(~ a + b + a:b , data=targets)
>
> then:
> summary(decideTests_eset_b_tmm)
>   [,1]
> -1 3343
> 0  9490
> 1  4191

You haven't actually told us which coefficient you're testing for.

> When having more than one factor, is it more appropriate to have the 
> interaction factor in the design?

Do you expect the effect of experimental factor b to be same for each 
level of a?  If yes, then maybe you don't need the interaction term.  It 
depends on your experiment and on the questions you want to ask.

> Thanks a lot
> Best,
>
> Fernando

BTW, I would much prefer it if you would post questions about edgeR to the 
main Bioconductor mailing list rather than to bioc-sig-sequencing.  The 
questions relate more to the general problem of analysing gene expression 
experiments rather than to details of particular sequencing technologies.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth

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