[BioC] get exprs from AffyBatch

James MacDonald jmacdon at med.umich.edu
Wed Feb 4 15:01:24 MET 2004

I'm not exactly sure what you are trying to do here, but I am going to
assume that you want to compute expression values for your genes, and
then export to a file.

The AffyBatch contains your raw PM and MM data, not expression values.
When you do

exp <- exprs(myAffyBatch)

You are simply creating a matrix of PM and MM values. To compute
expression values, you want to do something like 

eset <- rma(myAffyBatch)

see also ?expresso and ?mas5 for other ways to compute expression
values. Once you have run rma or whatever, you have an exprSet that can
be used with write.exprs() to export.

Note that the function you want is write.exprs() not exprs.write(). In
addition, you only have to pass the variable name of your exprSet and
the filename. I don't know if you actually used file=** and sep=*, but
you don't need sep (default is "\t", which is fine for most uses), and
file=** will give you a syntax error. You need something like
file="Expression values.txt"



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Hao Liu <liuha at umdnj.edu> 02/04/04 12:29AM >>>
I tried to use exprs to get expset by

> exp <- exprs(myAffyBatch)

I then tried to write:


however, I can't do this, seems exp is not really a 
expset object.

Best regards

Hao Liu, Ph. D

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