Yahb [guest] | 3 Jan 19:08 2013

GLM in DEseq


Dear all,
 I'm using DEseq to analyze differential expressed genes between 4 genotypes (A, B, C, D) under two
conditions (treated and untreated) with 2 replicates for each.
 I want to use the GLM in DEseq but I have a question.
 How can I retrieve the coefficients corresponding to the contribution of each factor (ie effect due to
genotype, due to treatment and the interaction between genotype and treatment) ?

My design is

	Treatment	Genotype
AU1	untreated	A
AU2	untreated	A
AT1	treated		A
AT2	treated		A
BU1	untreated	B
BU2	untreated	B
BT1	treated		B
BT2	treated		B
CU1	untreated	C
CU2	untreated	C
CT1	treated		C
CT2	treated		C
DU1	untreated	D
DU2	untreated	D
DT1	treated		D
DT2	treated		D

Code:

fit0a<- fitNbinomGLMs( cdsFull, count ~ Treatment)
fit0b<- fitNbinomGLMs( cdsFull, count ~ Genotype)
fit1<- fitNbinomGLMs( cdsFull, count ~ Treatment+Genotype)
fit2<- fitNbinomGLMs( cdsFull, count ~Treatment+Genotype+Treatment:Genotype)

#treatment effect
pvalW<-nbinomGLMTest( fit1,fit0b)
padjW<- p.adjust( pvalW, method="BH")

#genotype effect
pvalE<-nbinomGLMTest( fit1,fit0a)
padjE<- p.adjust( pvalE, method="BH")

#interaction treatment:genotype
pvalI <- nbinomGLMTest( fit2,fit1)
padjI <- p.adjust( pvalI, method="BH")

Thank you in advance
Best regards

 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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