[BioC] RE: gcrma

Christian.Stratowa at vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Wed Nov 26 17:10:33 MET 2003


Great, we are looking forward to test the new version
Christian


-----Original Message-----
From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu] 
Sent: Wednesday, November 26, 2003 17:05
To: Stratowa,Dr.,Christian FEX BIG-AT-V
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: gcrma


we have recently developed an approach to get around the slow numerical 
integration. by mid december it should be ready to use by others.

-r

On Wed, 26 Nov 2003 Christian.Stratowa at vie.boehringer-ingelheim.com wrote:

> Dear Dr. Irizarry
> 
> At the CHI meeting in Baltimore I enjoyed your interesting talk about 
> gcrma,
> 
> which currently seems to be the best algorithm for 
> condesation/normalization
> 
> of CEL files, as the affycomp results suggest. For this reason my 
> colleagues
> 
> and I were eager to test gcrma with our own datasets containing 
> between 20
> and 130 HGU133 chips.
> 
> My colleague tested rma and gcrma with the following setting: HP 
> xw8000 Dual Xeon 2.8 GHz with 2 GB RAM RedHat 8.0 with kernel 
> 2.4.18-SMP R-1.8.1 and Bioconductor 1.3 compiled by us for above 
> settings
> 
> Using this setup, rma can process the data really fast:
> 21 HGU133A data: about 1 minute
> 40 HGU133A data: about 1.5 minutes
> 130 HGU133A data: about 2.5 minutes
> 
> For gcrma we got the following results:
> 21 HGU133A data: about 45 minutes using 500 MB RAM
> 40 HGU133A data: about 90 minutes using 900 MB RAM
> 130 HGU133A data: the usual error: cannot allocate vector of size 
> blabla
> 
> Since we will soon switch to the new Affymetrix HG-U133_Plus_2 
> GeneChips, things will getting worse.
> 
> My questions are the following:
> Do you intend to optimize the behavior of gcrma, e.g. by rewriting it 
> in C? In the meantime, which setup would be sufficient for gcrma to 
> handle 130 HGU133A data? Do you think that a 64bit processor machine 
> would be helpful? Could the Dual G5 Mac be an option?
> 
> Thank you in advance for your help.
> P.S. Please reply also to me since I am not subscribed to the mailing 
> list.
> 
> Best regards
> Christian Stratowa
> 
> ==============================================
> Christian Stratowa, PhD
> Boehringer Ingelheim Austria
> Dept NCE Lead Discovery - Bioinformatics
> Dr. Boehringergasse 5-11
> A-1121 Vienna, Austria
> Tel.: ++43-1-80105-2470
> Fax: ++43-1-80105-2366
> email: christian.stratowa at vie.boehringer-ingelheim.com
> 
> 
>



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