Entering edit mode
David Martino
▴
10
@david-martino-3283
Last seen 10.2 years ago
Dear list,
I get an error:
"Error in contrasts.fit(fit,contrast.matrix):
Number of rows of contrast matrix must match number of
coefficients
In addition:
Warning row names don't match col names of coefficients"
for the following Timecourse design:
3 Timepoints
Stimulated (LPS) versus Unstimulated (CON) cells
Affy Gene1.0 chips
The targets are
ChipNumber Name Filename Time Treatment
Biolrep
1 LPS.0hr 0Hr_1.CEL 0 T
1
2 CON.0hr 0Hr_2.CEL 0 C
2
3 LPS.6hr 6HrLPS_1.CEL 6 T
3
4 LPS.6hr 6HrLPS_2.CEL 6 T
3
5 CON.6hr 6HrCon_1.CEL 6 C
4
6 CON.6hr 6HrCon_2.CEL 6 C
4
7 LPS.12hr 12HrLPS_1.CEL 12 T
5
8 LPS.12hr 12HrLPS_2.CEL 12 T
5
9 CON.12hr 12HrCon_1.CEL 12 C
6
10 CON.12hr 12HrCon_2.CEL 12 C
6
The design matrix is:
Targets<-readTargets()
lev<-c("LPS.0hr","CON.0hr","LPS.6hr",
+"CON.6hr","LPS.12hr","CON.12hr")
f<-factor(Targets$Name,levels=lev)
design<-model.matrix(~0+f)
colnames(design)<-lev
biolrep<-c(1,2,3,3,4,4,5,5,6,6)
corfit<-duplicateCorrelation(x,ndups=1,block=biolrep)
fit<-lmFit(,x,block=biolrep,cor=corfit$consensus)
fit<-eBayes(fit)
To extract the contrasts of interest:
cont.con<-makeContrasts("CON.6hr-CON.0hr","CON.12hr-
CON.6hr",levels=design)
cont.lps<-makeContrasts("LPS.6hr-LPS.0hr","LPS.12hr-
LPS.6hr",levels=design)
cont.dif<-makeContrasts(Dif6H=(LPS.6hr-LPS.0hr)-
+ (CON.6h-CON.0hr),Dif12H=(LPS.12hr-LPS.6hr)-
+ (CON.12hr-CON.6hr),levels=design)
cont.matrix<-cbind(cont.con,cont.lps,cont.dif)
The code:
fit2<-contrasts.fit(fit,cont.matrix)
returns the afforementioned error message.
Any input would be greatly appreciated.
With thanks,
David
sessionInfo(): R version 2.8.0 (2008-10-20)
