[BioC] limma package
yunie at caltech.edu
Wed Dec 10 20:15:56 MET 2003
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?
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