2007/8/5, Gordon K Smyth <smyth@wehi.edu.au>:
>
> >
> > It's just a list of log2 intensities even if is the output of
> > normalizeBetweenArrays function.
>
> I suspect you mean that it is a 'matrix'.  It cannot be of class
> 'list'.  Try
>
>   class(MA)


Yes, it's a matrix.

> In any data analysis, you should check you results at every step.  For
> >> example, have you looked at
> >> your normalized data?  What is the value of corfit$consensus?
> >
> > Yes,  I have  a corfit$consensus of 1.
>
> This means your data is degenerate in some way, so you cannot use
> duplicateCorrelation() without
> reworking your data.


This is interesting, I've found only few post about a corfit$consensus of 1,
but I haven't found a solution or a way to do.

I've  tried also avedups(), it's working but the result is always the same.
Should the problem be the design I'm using?

> design
  Cen15 Cen37 Cen97 Cen167 Cen618
1     1     0     0      0      0
2     0     1     0      0      0
3     0     0     1      0      0
4     0     0     0      1      0
5     0     0     0      0      1
attr(,"assign")
[1] 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$f
[1] "contr.treatment"

Thanks a lot

Francesco

-- 
Cancer Genomics Lab.
"Edo e Elvo Tempia" Foundation.
Via Malta 3 13900 Biella
Tel +39 015351830
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