Hi BioC,

I was runing eBayes and got the above error. I searched the old archives of BioC, and has found similar problem poseted by Ken Ninh: http://files.protsuggest.org/biocond/html/4652.html 

I checked the summary(fit$df.residual), all zero's. But the fit1<-lmFit(normData, design) and fit2<-contrasts.fit(fit1, cont.matrix) ran properly. I checked normData with boxplots, and they looked fine and well normalized. Here is my design matrix: 
 > design
      C.M.1 C.F.2 C.M.3 C.F.3 R.M.1 R.F.2 R.M.3 R.F.3 (C/R: control/treatment; F/M: male/female; 1,2,3 are sibling pairs)
1     1     0     0     0     0     0     0     0
2     0     1     0     0     0     0     0     0
3     0     0     1     0     0     0     0     0
4     0     0     0     1     0     0     0     0
5     0     0     0     0     1     0     0     0
6     0     0     0     0     0     1     0     0
7     0     0     0     0     0     0     1     0
8     0     0     0     0     0     0     0     1
attr(,"assign")
[1] 1 1 1 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$TBS
[1] "contr.treatment"

contrast matrix

> cont.matrix
      Diff
C.M.1   -1
C.F.2   -1
C.M.3   -1
C.F.3   -1
R.M.1    1
R.F.2    1
R.M.3    1
R.F.3    1

What could be the possible reasons for the error and how to fix that?

Thanks
Johnny


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