sequencing workshop

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.0 years ago

United States

Hi all, Just to let you know that the workshop, https://secure.bioconductor.org/SeattleNov08/ is now full. There is no waiting list. I am not sure if/when it will be offered again (just to head off questions). And yes, we will be posting materials on line for those that could not make it. thanks Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Cancer Cancer • 901 views

ADD COMMENT • link updated 15.5 years ago by Patrick Aboyoun ★ 1.6k • written 15.5 years ago by rgentleman ★ 5.5k

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caiwei@mdanderson.org ▴ 110

@caiweimdandersonorg-1599

Last seen 9.6 years ago

Dear all, I can use justRMA to read in 200+ U133_2 .Cel files and normalize at once on a sparc-sun-solaris2.9. with R version 2.7.0 (2008-04-22). I thought justMAS would be able to do similar task. But to use justMAS, we need to have an affybatch object first. read.affybatch fails with 100 arrays (can not allocate enough memory). are there other options to normalize 200+ U133-2 arrays all at once by MAS5? Thanks! Caimiao

ADD COMMENT • link 15.5 years ago caiwei@mdanderson.org ▴ 110

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If you have a computer cluster you also can use the package "affyPara". Then you have a very fast solution for large numbers of microarrays. Best Markus Wei,Caimiao wrote: > Dear all, > > I can use justRMA to read in 200+ U133_2 .Cel files and normalize at once on a sparc-sun-solaris2.9. with R version 2.7.0 (2008-04-22). > > I thought justMAS would be able to do similar task. But to use justMAS, we need to have an affybatch object first. read.affybatch fails with 100 arrays (can not allocate enough memory). > > are there other options to normalize 200+ U133-2 arrays all at once by MAS5? > > Thanks! > > Caimiao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

ADD REPLY • link 15.5 years ago Markus Schmidberger ▴ 380

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Yes, you could for example use package "xps" available from BioConductor, or alternatively package "aroma.affymetrix". Regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ Wei,Caimiao wrote: > Dear all, > > I can use justRMA to read in 200+ U133_2 .Cel files and normalize at once on a sparc-sun-solaris2.9. with R version 2.7.0 (2008-04-22). > > I thought justMAS would be able to do similar task. But to use justMAS, we need to have an affybatch object first. read.affybatch fails with 100 arrays (can not allocate enough memory). > > are there other options to normalize 200+ U133-2 arrays all at once by MAS5? > > Thanks! > > Caimiao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >

ADD REPLY • link 15.5 years ago cstrato ★ 3.9k

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Patrick Aboyoun ★ 1.6k

@patrick-aboyoun-6734

Last seen 9.6 years ago

United States

Hi folks, Due to popular demand, we had added 5 seats to the Nov 12-14 sequencing short course at the Fred Hutchinson Cancer Research Center. To enroll in this course, please fill out the registration form at https://secure.bioconductor.org/SeattleNov08/ We anticipate that these seats will fill up fast, so enroll today. Patrick

ADD COMMENT • link 15.5 years ago Patrick Aboyoun ★ 1.6k

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