[BioC] LIMMA error: No residual degrees of freedom

[Saurin Jani]

Hi ,

I have 4 CEL files and each one is in different Group.
I am doing ReadAffy() and RMA
 
> pData(myRMA);
     sample   pheno1 pheno2
A       1     Group1      1
B       2     Group2      2
C       3     Group3      3
D       4     Group4      4


> design <- model.matrix(~ 0 +factor(c(1,2,3,4)));
> colnames(design) <-
c("Group1","Group2","Group3","Group4");
> fit <- lmFit(myRMA,design);
> contrast.matrix1 <-
makeContrasts(Group2-Group1,Group3-Group4,Group2-Group3,Group4-Group1,Group3-Group1,Group4-Group2,levels
= design);
> fitM1 <- contrasts.fit(fit,contrast.matrix1);
> fitM1<- eBayes(fitM1);
Error in ebayes(fit = fit, proportion = proportion,
stdev.coef.lim = stdev.coef.lim) :
        No residual degrees of freedom in linear model
fits


Any suggestion will be great,

Thank you,
Saurin




		
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