[BioC] lmfit "No residual degrees of freedom"

[David martin]

Hello,
I'm having problems computing comparisons between different groups (this 
is not array data and i'm not using limma). Any on what the error must be ?

 > mydata.eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 2754598 features, 3 samples
   element names: exprs
protocolData: none
phenoData
   sampleNames: sampleA sampleB sampleC
   varLabels: Group Sample
   varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:


fit <- lmFit(mydata.eset, design)
....
contrast.matrix
 > contrast.matrix
                     group1-group2
group1                                   1
group2                                      -1
group3                                       0
                     group1-group3
group1                                   1
group2                                       0
group3                                      -1
                     group2-group3
group1                               0
group2                                   1
group3                                  -1

fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = 
stdev.coef.lim) :
   No residual degrees of freedom in linear model fits

thanks,
david