[BioC] limma package

Susan Holmes susan at stat.stanford.edu
Wed Dec 10 20:52:25 MET 2003

Agilent's extraction software also provides a flat file with
all the meaurements, median and mean background and foregounds,
so you can use those as an input,
I found this very amenable to use of Bioconductor
in what I do,
Susan Holmes
Associate Professor

On Wed, 10 Dec 2003, Anna Cao wrote:

> 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
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