RE: gcrma
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@christianstratowavieboehringer-ingelheimcom-545
Last seen 7.3 years ago
Great, we are looking forward to test the new version Christian -----Original Message----- From: Rafael A. Irizarry [mailto:ririzarr@jhsph.edu] Sent: Wednesday, November 26, 2003 17:05 To: Stratowa,Dr.,Christian FEX BIG-AT-V Cc: bioconductor@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@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@vie.boehringer-ingelheim.com > > >
hgu133a affycomp gcrma PROcess hgu133a affycomp gcrma PROcess • 473 views

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