Microarray contrast matrix design
1
1
Entering edit mode
10.0 years ago
c12i34 ▴ 30

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

microarray r • 3.5k views
ADD COMMENT
0
Entering edit mode
10.0 years ago
Manvendra Singh ★ 2.2k

You have a data frame where first three columns are Normal and then next two columns are"stage1_cancer" and next three columns 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

Login before adding your answer.

Traffic: 1713 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6