[BioC] One-Color Agilent miRNA microarrays

[Gordon K Smyth]

On Wed, August 8, 2007 11:10 pm, Francesco Favero wrote:
> 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

Yes, the problem certainly is the design matrix you're using.  Your design matrix implies that you
have 5 different treatments applied to 5 arrays.  In other words, you have no replication, so that
no statistical analysis is possible.

Please have a look at the limma User's Guide on different types of designs, and think about what
type of experiment you really have.

Best wishes
Gordon