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Question: Microarray contrast matrix design
1
gravatar for c12i34
6.3 years ago by
c12i34 • 20
United Kingdom
c12i34 • 20 wrote:

Hi I am trying to create an appropriate design matrix to determine gene that are differentially expressed between cancer and normal sample. Below table is the information file for my dataset.

Sample Subtype Cancer
A Normal Normal
B Normal Normal
C Normal Normal
D stage 1 Cancer
E stage 1 Cancer
F stage 2 Cancer
G stage 2 Cancer
H stage 2 Cancer
I NA Biopsy

At the moment I create a design matrix using these command:

f=factor(information$cancer)
design=model.matrix(~f)
fit=lmFit(exp_sample,design)
fit=eBayes(fit)

However I am not sure how to construct my contrast matrix for 2 levels (compare cancer and normal) only? Also do i need to discard those biopsy data or not? It would be great if you guys can give me some advice! Many thanks
microaray R • 2.8k views
ADD COMMENT • link •
modified 6.3 years ago by Manvendra Singh • 2.1k • written 6.3 years ago by c12i34 • 20
0
gravatar for Manvendra Singh
6.3 years ago by
Manvendra Singh • 2.1k
Berlin, Germany
Manvendra Singh • 2.1k wrote:

you have dataframe where first three coloumns are Normal and then next two coloumns are"stage1_cancer" and next three coloumns are "stage3_cancer" carrying their respective expression values. (here we discard biopsy) you should then do it like following :

 

groups<-as.factor(c(rep("Normal",3),rep("stage1_Cancer",2), rep("stage2_Cancer",3)))
design<-model.matrix(~0+groups)
colnames(design)=levels(groups)
fit<-lmFit(dataframe, design)
cont.matrix.stage2<-makeContrasts(stage2_Cancer-Normal,
levels=design)
cont.matrix.stage1<-makeContrasts(stage1_Cancer-Normal,
levels=design)
fit.stage2<-contrasts.fit(fit, cont.matrix.stage2)
fit.stage1<-contrasts.fit(fit, cont.matrix.stage1)
ebfit.stage2<-eBayes(fit.stage2)
ebfit.stage1<-eBayes(fit.stage1)
topTable.stage2(ebfit.stage2, number=Inf, p=0.05, adjust.method="none", coef=1)
topTable.stage1(ebfit.stage1, number=Inf, p=0.05, adjust.method="none", coef=1)

 
ADD COMMENT • link written 6.3 years ago by Manvendra Singh • 2.1k
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