[BioC] Annalyzing replicates in the Agilent chip 4 x44 with limma

[Francois Pepin]

Hi Ester,

I do not think this is possible to do with Limma, short of doing a fair
amount of hacking around in limma itself.

In my experience the replicate probes in Agilent arrays behave almost
identically (as opposed to different probes for a same gene). For
simplicity's sake, we just use any one of them as representative. You
could also take the average if you wanted.

In my opinion, unless you see significant variations between those
probes doing more than that would not be worth the effort.

Francois

On Wed, 2007-07-11 at 16:14 +0300, Ester Feldmesser wrote:
> Hi everybody,
>  
> The human Agilent chip 4x44 has most of the probes only once, but some 
> of then appear in 10 replicates. These replicates are genes and not 
> controls.
> I am using the Limma package to analyze them. I would like to define 
> these replicates as technical ones and leave the other probes (those 
> that appear once) as they are.
> What is the best way to define only part of the spots as replicates?
> 
> Thanks for your help
> Esti