[BioC] Raw, summarized intensity data from CEL files

[James W. MacDonald]

Or better yet, just use gcrma(). There is an argument for normalization 
(set to TRUE by default), and if you don't want things logged, just 
'un-log' them. For instance

mydata <- gcrma(abatch, normalize = FALSE)
exprs(mydata) <- 2^exprs(mydata)

Best,

Jim



Naomi Altman wrote:
> Have a look at expresso.  It allows you control over all aspects of the 
> normalization and summarization process.
> 
> --Naomi
> 
> At 12:17 PM 7/14/2008, Niels Høgslund wrote:
>> Dear list,
>>
>> Can anybody suggest a way in which I can get background-corrected and
>> summarized (gcrma style), but unnormalized and unlogged data from a
>> batch of CEL files?
>>
>> ....apologies if I´m overlooking something obvious here!
>>
>> Thanks in advance,
>>
>> Niels
>>
>>
>>
>>
>> Niels Høgslund
>> BiRC -Bioinformatics Research Center
>> Høegh-Guldbergs Gade 10
>> DK-8000 Århus C
>> Denmark
>> phone: +45 89423100
>> mail: nj at birc.au.dk
>>
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> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623