[BioC] RankProd analysis for Agilent Single Color array ??

[neeraj [guest]]

hi,

i am doing one color agilent arrays..i have three groups,GROUP1,GROUP2,GROUP3 and each group has 4 replicates.i made contrast matrix using limma.Is this possible to analyse data by RankProd using same contrast matrix.
i want to make comparison by RankProd as
GROUP1 vs GROUP2
GROUP1 vs GROUP3
GROUP3 vs GROUP2

plz let me know if there is any way to do it in single command using RankProd as we can do it in limma.

this is the R-script i used.

 targets
   SampleNumber                     FileName Condition
1             1  K_BNG202_251485068094_1.txt     GROUP1
2             2  K_BNG211_251485067236_1.txt     GROUP1
3             3  K_BNG252_251485068096_1.txt     GROUP1
4             4  K_BNG263_251485068028_1.txt     GROUP1
5             5  P_BNG019_251485068025_3.txt     GROUP2
6             6  P_BNG039_251485066211_1.txt     GROUP2
7             7  P_BNG065_251485068023_4.txt     GROUP2
8             8  P_BNG076_251485068021_4.txt     GROUP2
9             9  V_BNG264_251485068028_2.txt      GROUP3
10           10  V_BNG271_251485068092_1.txt      GROUP3
11           11 V_BNG_043_251485037342_2.txt      GROUP3
12           12 V_BNG_089_251485037359_3.txt      GROUP3
> colnames(y.q[j,])
 [1] "K_BNG202_251485068094_1"  "K_BNG211_251485067236_1"  "K_BNG252_251485068096_1" 
 [4] "K_BNG263_251485068028_1"  "P_BNG019_251485068025_3"  "P_BNG039_251485066211_1" 
 [7] "P_BNG065_251485068023_4"  "P_BNG076_251485068021_4"  "V_BNG264_251485068028_2" 
[10] "V_BNG271_251485068092_1"  "V_BNG_043_251485037342_2" "V_BNG_089_251485037359_3"
> design <- model.matrix(~0 + f)
Error in eval(expr, envir, enclos) : object 'f' not found
> f <- factor(targets$Condition, levels = unique(targets$Condition))
> design <- model.matrix(~0 + f)
> colnames(design) <- levels(f)
> contrast.matrix <- makeContrasts("GROUP1-GROUP2", "GROUP2-GROUP3", "GROUP3-GROUP1", levels=design)






 -- output of sessionInfo(): 

 R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RankProd_2.30.0 limma_3.4.3 

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