[BioC] get exprs from AffyBatch

[Hao Liu]

I got this message using mas5:

mascolon <- mas5(myAffyBatch,normalize=TRUE, sc=150,
analysis="ablolute");
background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...Error: cannot allocate vector of size 585042 Kb

My AffyBatch has 151 samples, could this be the problem?

Thanks a lot for your kind replies.

Best
Hao

-----Original Message-----
From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu] 
Sent: 2004Äê2ÔÂ4ÈÕ 11:18
To: James MacDonald
Cc: bioconductor at stat.math.ethz.ch; liuha at umdnj.edu
Subject: Re: [BioC] get exprs from AffyBatch


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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