Hi,

I am carrying out a multifactorial analysis on edgeR according to the 
experimental design shown at the end of this message (which I called 
design.all).

My reference genotype being "Col", I created the following model matrix 
and its subsequent glmFit model, in order to see for expression 
modulation according to genotype, time, as well as their interaction:

matrix.all<- model.matrix(~gtype*time, data=design.all)
colnames(matrix.all)
# [1] 
"(Intercept)""gtypeOE1""gtypeR24""gtypeX710""timeT1.5""timeT3""timeT6""gtypeOE1:timeT1.5" 

# [9] "gtypeR24:timeT1.5""gtypeX710:timeT1.5" 
"gtypeOE1:timeT3""gtypeR24:timeT3""gtypeX710:timeT3""gtypeOE1:timeT6""gtypeR24:timeT6""gtypeX710:timeT6"
fit.all <- glmFit (dge.all, matrix.all)

Following the 3.3.4 section of the user guide, I carried on as follows:

lrt.all.gtype <- glmLRT(fit.all, coef=2:4)
lrt.all.time<- glmLRT(fit.all, coef=5:7)
lrt.all.inter <- glmLRT(fit.all, coef=8:16)

Which leaves me with two questions that remain unclear to me:
1-Section 3.3.4. of the user guide states that coefficients 3 and 4 of 
the depicted example correspond to "the effects of the placebo at 1 hour 
and 2 hours". Why just placebo? Does not it include the "Drug". In my 
case, do coefficients 5 to 7 hence refer to "Col" at different times? Do 
they not include the other genotypes at the corresponding times?
2-Concerning the interaction, why does neither "Col" nor "T0" appear on 
the coefficients? Should not they be part of the comparison? Do I not 
need them to follow the difference between genotypes in time? Section 
3.3.4.states that "(coef=5:6)...detects genes that respond differently 
to the drug, relative to the placebo, at either of the times (i.e.1h and 2h)

I thank you any help you could provide me on this. Thank you for your work.

Kind regards,

David Rengel



	

gtype

	

time

Col.T0.R2

	

Col

	

T0

Col.T0.R3

	

Col

	

T0

Col.T1.5.R1

	

Col

	

T1.5

Col.T1.5.R2

	

Col

	

T1.5

Col.T1.5.R3

	

Col

	

T1.5

Col.T3.R1

	

Col

	

T3

Col.T3.R2

	

Col

	

T3

Col.T3.R3

	

Col

	

T3

Col.T6.R1

	

Col

	

T6

Col.T6.R2

	

Col

	

T6

Col.T6.R3

	

Col

	

T6

OE1.T0.R2

	

OE1

	

T0

OE1.T0.R3

	

OE1

	

T0

OE1.T1.5.R1

	

OE1

	

T1.5

OE1.T1.5.R2

	

OE1

	

T1.5

OE1.T1.5.R3

	

OE1

	

T1.5

OE1.T3.R1

	

OE1

	

T3

OE1.T3.R2

	

OE1

	

T3

OE1.T3.R3

	

OE1

	

T3

OE1.T6.R1

	

OE1

	

T6

OE1.T6.R2

	

OE1

	

T6

OE1.T6.R3

	

OE1

	

T6

R24.T0.R2

	

R24

	

T0

R24.T0.R3

	

R24

	

T0

R24.T1.5.R1

	

R24

	

T1.5

R24.T1.5.R2

	

R24

	

T1.5

R24.T1.5.R3

	

R24

	

T1.5

R24.T3.R1

	

R24

	

T3

R24.T3.R2

	

R24

	

T3

R24.T3.R3

	

R24

	

T3

R24.T6.R1

	

R24

	

T6

R24.T6.R2

	

R24

	

T6

R24.T6.R3

	

R24

	

T6

710.T0.R2

	

X710

	

T0

710.T0.R3

	

X710

	

T0

710.T1.5.R1

	

X710

	

T1.5

710.T1.5.R2

	

X710

	

T1.5

710.T1.5.R3

	

X710

	

T1.5

710.T3.R1

	

X710

	

T3

710.T3.R2

	

X710

	

T3

710.T3.R3

	

X710

	

T3

710.T6.R1

	

X710

	

T6

710.T6.R2

	

X710

	

T6

710.T6.R3

	

X710

	

T6

-- 
David Rengel
Laboratoire des Interactions Plantes Micro-organismes (LIPM)
INRA/CNRS
24 Chemin de Borde Rouge
Auzeville
CS 52627
31326 Castanet Tolosan Cedex

E mail: david.rengel@toulouse.inra.fr
Tel 33 (0)5 61 28 55 91
Fax 33 (0)5 61 28 50 61

http://www.toulouse.inra.fr/lipm


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