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Last seen 9.6 years ago
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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