[BioC] limma package

[Anna Cao]

Hi,

I'm trying to normalize between arrays using the limmma package so I 
can run SAM. I want to know whether we can read log2 ratio data into 
R? I'm using Agilent's extraction program to extract cDNA arrays 
data and the image analysis program from Agilent automatically 
normalize within array, giving the normalized intensity and log 
ratio. Is there anyway I can by-pass reading Mean/Median foreground 
and background intensity and directly feed the processed (background 
subtracted and normalized) intensity into R?

Another question: Can I also input a column that filters spots which 
were unsatisfactory according to the image analysis program? And how 
can I can remove these bad spots from further calculation in R using 
the limma package or any other functions in R?

Thanks,

Anna