[BioC] how to use limma on this format

[Sean Davis]

Weiwei Shi wrote:
> Hi,
> 
> I tried "agilent" and it works!!! The situation is like this: the data
> provider does not give me any hint about the "source" and I did not
> try.
> 
> A further question here is, if I want to continue with Quality
> Assessment procedures, is there any online materials I can following
> by using limma? (is limma's User's guide good for that purpose).
> 
> I knew there is a spot quality weight function and I am wondering
> which column servers that purpose.
> 
> I am quite newbie for QC for Agilent data. Thanks for any suggestions!
>

You will probably want to get the manual for the Agilent Feature
Extraction software to review the definitions of the columns (available
from Agilent or on the computer on which the slides were scanned).
Agilent provides copious information for use in quality assessment.
Generally speaking, though, you have two-color data and many of the
principles are the same as for other two-color array systems.

Sean