[BioC] LIMMA error: No residual degrees of freedom

[James W. MacDonald]

Saurin Jani wrote:
> Hi ,
> 
> I have 4 CEL files and each one is in different Group.
> I am doing ReadAffy() and RMA

With only one sample per group you cannot fit a model because you have 
no replication (hence, no residual degrees of freedom). You will only be 
able to compute fold changes.


>  
> 
>>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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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109