R help - Nov 2007 - need help with error message:Error in lm.fit(design, t(M)) : incompatible dimensions

Hello,

 

I am trying to run a code (see reference section) and when I run the line:

fit<-lmFit(xen1dataeset,design),

 

 I get the error message: Error in lm.fit(design, t(M)) : incompatible
dimensions

 

I will really appreciate if someone can help me understand this error
message and possibly help me debug the problem.

 

Thanks

manisha

 

Reference section

 

xen1data<-ReadAffy() # Read Affy dataset cell files

 

xen1dataeset<-gcrma(xen1data) # Normalize with GCRMA

 

write.exprs(xen1dataeset,file="xen1_exprs") # write normalzed
expression
values

 
>str(exprs(xen1dataeset))
num [1:22690, 1:2] 12.0 11.3 13.0 11.6 10.3 ...

 - attr(*, "dimnames")=List of 2

  ..$ : chr [1:22690] "1415670_at" "1415671_at"
"1415672_at" "1415673_at"
...

  ..$ : chr [1:2] "A1_xen1_1_1.CEL" "A2_xen2a_5_2.CEL"

 

targets<-readTargets("xen1shrt.txt") # Read target files
>targets
 

  Name         FileName Target

1  A1_xen1_1_1  A1_xen1_1_1.CEL  A_xen

2 A2_xen2a_5_2 A2_xen2a_5_2.CEL  A_xen

3 A3_xen2b_6_3 A3_xen2b_6_3.CEL  A_xen

4   B1_cr1_2_4   B1_cr1_2_4.CEL  B_crp

5  B2_cr2a_9_5  B2_cr2a_9_5.CEL  B_crp

6 B3_cr2b_10_6 B3_cr2b_10_6.CEL  B_crp

 

f<-factor(targets$Target,levels=c("A_xen", "B_crp"))  #
Define levels
>f
 

[1] A_xen A_xen A_xen B_crp B_crp B_crp

Levels: A_xen B_crp

 

design<-model.matrix(~0+f) # Define design matrix based on Factors

 
>design
 

  A_xen B_crp

1     1     0

2     1     0

3     1     0

4     0     1

5     0     1

6     0     1

attr(,"assign")

[1] 1 1

attr(,"contrasts")

attr(,"contrasts")$f

[1] "contr.treatment"

 

colnames(design)<- c("A_xen", "B_crp") # Define colnames
of the design
matrix

 

fit<-lmFit(xen1dataeset,design) # Fit linear model based on the design
matrix

 

contrast.matrix<- makeContrasts(B_crp- A_xen) # define contrast matrix

 

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

 

fit3<-eBayes(fit2) # Calculate B and P-values for contrast

 

crpMxen<-topTable(fit3,coef=1,number=22690,adjust.method="BH",sort.by='B')

 

 

 


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