[BioC] get exprs from AffyBatch

[Rafael A. Irizarry]

i would like to add to jim's suggestion that
there is also 

exprs2excel (myAffyBatch)

for creation of excel compatible files.


On Wed, 4 Feb 2004, James MacDonald wrote:

> 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"
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> 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:
> 
> exprs.write(exp,file=**,sep=*)
> 
> however, I can't do this, seems exp is not really a 
> expset object.
> 
> 
> 
> Best regards
> 
> Hao Liu, Ph. D
> 
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