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Nolwenn Le Meur
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@nolwenn-le-meur-888
Last seen 10.1 years ago
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.name
s=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=f
it,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
Facult? de m?decine
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@nantes.inserm.fr