[BioC] Need help in Anova design (contrast.tratment)

[ashwin Vishnuvardhana]

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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Type	Filename	Gender
1Mut-F1	1Mut-F1.CEL	F
1Mut-F3	1Mut-F3.CEL	F
1Mut-M4	1Mut-M4.CEL	M
1Mut-M5	1Mut-M5.CEL	M
6 WT-F2	6 WT-F2.CEL	F
6 WT-F3	6 WT-F3.CEL	F
6 WT- M2	6 WT- M2.CEL	M
6 WT - M3	6 WT - M3.CEL	M
24 WT-F4	24 WT-F4.CEL	F
24 WT-M3	24 WT-M3.CEL	M
24 WT-M4	24 WT-M4.CEL	M
101Mut -F1	101Mut -F1.CEL	F
101Mut -F2	101Mut -F2.CEL	F
101Mut -M1	101Mut -M1.CEL	M
101Mut-M2	101Mut-M2.CEL	M
Non-Tg-M1	Non-Tg-M1.CEL	M
Non-Tg-M2	"Non-Tg-M2,CEL"	M
Non-Tg-F2	Non-Tg-F2.CEL	F
Non-Tg-F3	Non-Tg-F3.CEL	F