[BioC] need help in Contrast. Treatment design

[Vishnuvardhana, Ashwin [BSD] - SRF]

Hi,

I am working on 2x2 Factorial Experiment(ANOVA With interaction factor)and following Limma user guide( chapter 11.4 Estrogen Data). Basically I am interested in knowing how "gender" variable is effecting outcome of experiment(please see attached file for sample information)  is effecting  

But I am getting error at 

"colnames(design)"

Error in dimnames(x) <- dn :   length of 'dimnames' [2] not equal to array extent

 

This is list of R codes that I ran for getting to this point 

 

Þ     targets <- readTargets("phenoData.txt",sep=",",row.names="filename")

Þ     contrasts(treatments) <- cbind(Type=c(0,0,0,0,1,1),MMut=c(0,1,0,0,0,0),FWT=c(0,0,1,0,0,0),MWT =c(1,0,0,0,0,0),FMut=c(0,0,0,1,0,0),NonTgM=c(0,0,0,0,0,1),NonTgF=c(0,0,0,0,1,0)) 

Þ     > contrasts(treatments) 

Þ            Gender MMut FWT MWT FMut

Þ     MMut        0    0   0   1    0

Þ     MWT         0    1   0   0    0

Þ     FMut        0    0   1   0    0

Þ     FWT         0    0   0   0    1

Þ     NonTGM      1    0   0   0    0

Þ     NonTGF      1    0   0   0    0

> design <- model. Matrix(~treatments)

> design 

   (Intercept) treatments Type treatmentsMMut treatmentsFWT treatmentsMWT treatmentsFMut

1            1              0              0             0             1              0

2            1              0              0             0             1              0

3            1              0              0             0             1              0

4            1              0              0             0             1              0

5            1              0              1             0             0              0

6            1              0              1             0             0              0

7            1              0              1             0             0              0

8            1              0              1             0             0              0

9            1              0              0             1             0              0

10           1              0              0             1             0              0

11           1              0              0             1             0              0

12           1              0              0             1             0              0

13           1              0              0             0             0              1

14           1              0              0             0             0              1

15           1              0              0             0             0              1

16           1              0              0             0             0              1

17           1              1              0             0             0              0

18           1              1              0             0             0              0

19           1              1              0             0             0              0

20           1              1              0             0             0              0

21           1              1              0             0             0              0

22           1              1              0             0             0              0

23           1              1              0             0             0              0

24           1              1              0             0             0              0

 

Any help is greatly appreciated.

 

Ash

 

 

 

 

 



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