Hi, I am using the gcrma function to calculate genechips intensities. I realize that it requires a lot of RAM and takes quite a lot of time to compute the intensities related to more then 11 arrays on a Pentium IV 2.5 GHz, 1 Gb RAM running RedHat 8.0. Since I am setting up a little linux cluster I wonder if there is any possibility to distribute the gcma calculation over a PC cluster. Raffaele -- Prof. Raffaele A. Calogero Unit? di Genomica e Bioinformatica Dipartimento di Scienze Cliniche e Biologiche Universit? di Torino Ospedale S. Luigi, Regione Gonzole 10 10043 Orbassano (TO) Italy Office Tel ++39 0116708110 Office Fax ++39 fax 0112368110 Department Fax ++39 0119038639 mobile Phone ++39 3333827080 email raffaele.calogero@unito.it www: www.bioinformatica.unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex

Raffaele Calogero <raffaele.calogero@unito.it> writes: > I am using the gcrma function to calculate genechips intensities. I > realize that it requires a lot of RAM and takes quite a lot of time > to compute the intensities related to more then 11 arrays on a Pentium > IV 2.5 GHz, 1 Gb RAM running RedHat 8.0. > Since I am setting up a little linux cluster I wonder if there is any > possibility to distribute the gcma calculation over a PC cluster. Not yet, though there is some interest in parallelizing some of the normalization routines (gcrma, vsn) via the compute-cluster extensions to R using pvm/lam-mpi. best, -tony -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

there is. the slowness comes from 200,000 numeric integrations. they are "embarasingly parallel". however, i would wait until version 1.0 when we hope to have more efficient procedures. On Sun, 5 Oct 2003, Raffaele Calogero wrote: > Hi, > I am using the gcrma function to calculate genechips intensities. I > realize that it requires a lot of RAM and takes quite a lot of time to > compute the intensities related to more then 11 arrays on a Pentium IV > 2.5 GHz, 1 Gb RAM running RedHat 8.0. > Since I am setting up a little linux cluster I wonder if there is any > possibility to distribute the gcma calculation over a PC cluster. > Raffaele > > -- > > Prof. Raffaele A. Calogero > Unitŕ di Genomica e Bioinformatica > Dipartimento di Scienze Cliniche e Biologiche > Universitŕ di Torino > Ospedale S. Luigi, Regione Gonzole 10 > 10043 Orbassano (TO) Italy > Office Tel ++39 0116708110 > Office Fax ++39 fax 0112368110 > Department Fax ++39 0119038639 > mobile Phone ++39 3333827080 > email raffaele.calogero@unito.it > www: www.bioinformatica.unito.it > > > > > _____________________________________________________________________ > For your security, this mail has been scanned and protected by Inflex > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >