[BioC] RE: How to fit patient as a fixed effect/paired samples

[PJARES at clinic.ub.es]

I am using affymetrix arrays to study primary and
metastic tumors from the same patients (five patients,
so five primary and five metastatic tumors). As we
have two classes and paired experiments I have been
using a paired t-test. However, I would like to use
limma with my arrays.


It seems that one can fit patient as a fixed effect in order to limma
compute paired t-tests with moderated denominators.
How to fit patient as a fixed effect? It would be by adding it in the
phenotable.


tmp<-pData(eset)

tmp<-cbind(tmp,TumorMetastasis=factor(c(0,1,0,1,0,1,0,1,0,1)))

tmp<-cbind(tmp,BLOCKpaireddata=factor(c(1,1,2,2,3,3,4,4,5,5)))

pData(eset)<-tmp

 

and then

 

design<-model.matrix(~TumorMetastasis*BLOCKpaireddata, data=pData(eset))


fit<-lmFit(eset,design)

contrast.matrix<-makeContrasts(Tumor_Metastasis,levels=design)

fit2<-contrasts.fit(fit,contrast.matrix)

 

Thank you very much for your help,

Best wishes,

 

Pedro


Pedro Jares, Ph.D.
Genomics Unit, IDIBAPS
University of Barcelona
C/ Villarroel 170
08036, Barcelona, Spain
Telf 93 2275400
Ext. 2184 o 2129
Fax 93 2275717