Hi all,

I am using DMRcate to find differentially methylated regions in illumina 450k data between one group of 4 samples and another group of 9 samples.

I followed all the steps of DMRcate user's guide and I build the design matrix in a similar manner,

and this is it:

str(design)
 num [1:13, 1:14] 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:13] "1" "2" "3" "4" ...
  ..$ : chr [1:14] "(Intercept)" "patient020" "patient021" "patient023" ...
 - attr(*, "assign")= int [1:14] 0 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "contrasts")=List of 2
  ..$ patient: chr "contr.treatment"
  ..$ type   : chr "contr.treatment"

But when I call the cpg.annotate(), I have this error:

myannotation <- cpg.annotate(myMvalue, analysis.type = "differential", design = design, coef = 14)
Coefficients not estimable: typeGroup2
Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  :
  No residual degrees of freedom in linear model fits
Inoltre: Warning message:
Partial NA coefficients for 425827 probe(s) 

In the DMRcate example dataset, that I have tested, the differential analysis is paired 38 vs 38

and I think that the error probably is in the design matrix building of my dataset.

So how to set the design matrix correctly?

Thanks in advance, Regards

Giovanni