[BioC] edgeR: glmLRT test
James W. MacDonald
jmacdon at uw.edu
Fri Mar 22 15:17:18 CET 2013
The short answer is that it doesn't matter, contingent upon you having
set up the experiment correctly. Have you tried constructing the design
matrix each way?
> phenotype <- factor(rep(1:2, each=8))
> area <- factor(rep(1:2, times = 8))
 "(Intercept)" "area2" "phenotype2"
 "(Intercept)" "phenotype2" "area2"
The interpretation of each coefficient will be the same in both instances.
On 3/22/2013 9:57 AM, KJ Lim wrote:
> Dear edgeR community,
> Good day.
> I have sets of RNA-Seq data of 2 phenotype (HighS, LowS) plants with area
> TZ& SW (control). I used exactTest to study which genes that are
> differential expressed in area TZ compare to SW of each phenotype.
> I would like to know do the phenotypes have effect on the area, in this
> case I should use glmLRT test. Before fit into the GLM, I defined my design
> matrix as:
> Could someone please advice me regarding the design matrix? Should I define
> my design matrix as ~area+phenotype ?
> Thank you very much for your time and help.
> Have a nice weekend.
> Best regards,
> KJ Lim
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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