question about LIMMA

Hello all,

I am a PhD student at University of Pisa.
I frequently use LIMMA package to handle gene expression microarray data.
I have a question about spot copies management by LIMMA.
I know that LIMMA needs all spots on the array are in the same number of copy ( e.g. each spot in double ).
In my research group It is just starting a project in wich we use Agilent microarrays (so high density
microarrays) and on these arrays there is only a block of probes,  positioned in a random fashion, in more
than one spot for each probe. Moreover there is not the same number of copies for each probe in this block.
Is LIMMA able to manage this situation?
That is, is LIMMA able to use this kind of random replicated spots to perform a quality control procedure, to
fit the linear model and to produce a unique fold change value for this probe?
Can I use any kind of strategy to solve this problem?
Does It exists a free package that does this?

Thank you very much for any information about this topic.

Best Regards

Erika Melissari
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