[BioC] Limma and drug treatment

[Nolwenn Le Meur]

Dear all,

I would like to found out if there is an interaction between treatments
(Amines and Betabloc) on gene expression. I would like to known if some
genes are differentially expressed by one of
the drugs(Betabloc,Amines) or their combination (Betabloc:Amines). Reading
the Bioconductor FAQ I think that these questions can be answered by Limma
but I am not sure of
what I get for result with the following script.

The design matrix only gives me the first topres (diffrentially expressed)
genes for the  clinical parameter "Betabloc".
How can I get the data for the Betabloc:Amines relationship.
Do I have to write a specific design matrix like
design<-model.matrix(~Betabloc:Amines-1,data=pData(clinicFull)) ?

Does the following contrast matrix give me the genes differentially
expressed between patients taking "Betabloc" and the one taking "Amines" ?

Thank you in advance,Best regards,
Nolwenn Le Meur


##Code
VD<-read.table("VD.txt",header=TRUE,sep="\t",row.names=1)
 clinicFull<-read.phenoData("clinic.txt",header=TRUE,sep="\t",row.names=1)
 eset<-new("exprSet",exprs=VD1,phenoData= clinicFull)
eset

#Expression Set (exprSet) with
#        571 genes
#        94 samples
#                 phenoData object with 18 variables and 94 cases
#         varLabels
#                SampleID: read from file
#                CODEBDD: read from file
#                PAT: read from file
#                SEXE: read from file
#                Tabac: read from file
#                Diabete: read from file
#                HTA: read from file
#                Ifam: read from file
#                Dyslipid: read from file
#                IEC: read from file
#                Betabloc: read from file
#                Amines: read from file
#                Inh: read from file
#                Antialdo: read from file
#                duir: read from file
#                statine: read from file
#                amio: read from file
#                digi: read from file

##Model Betabloc+Amines+Betabloc:Amines
design<-model.matrix(~Betabloc*Amines-1,data=pData(clinicFull))
fit <- lmFit(eset, design)
eb<-ebayes(fit)
topres<-toptable(number=571,genelist=as.character(row.names(VD)),fit=fit,eb=
eb,adjust="holm")
length(which(topres$P.Value<0.01))

cont.matrix<-makeContrasts(Betabloc-Amines,levels=design)
fit1<-contrasts.fit(fit,cont.matrix)
eb1<-ebayes(fit1)
topres1<-toptable(number=571,genelist=as.character(row.names(VD)),fit=fit1,e
b=eb1,adjust="holm")
length(which(topres1$P.Value<0.01))


********************************************
Nolwenn Le Meur
INSERM U533
Faculté de médecine
1, rue Gaston Veil
44035 Nantes Cedex 1
France

Tel: (+33)-2-40-41-29-86 (office)
     (+33)-2-40-41-28-44 (secretary)
Fax: (+33)-2-40-41-29-50
mail: nolwenn.lemeur at nantes.inserm.fr