Is there a standard workflow to produce RMA/PLM chip pseudo images, NUSE, RLE plots and the like for HuGene 1.0 ST arrays in xps? I think creating an AffyBatch object may be the way to go, but I'd like to confirm this first before figuring out how to create one. Will this run into memory issues? Regards, _Taku Taku A. Tokuyasu, PhD Computational Biologist Biostatistics and Computational Biology Core UCSF, Box 0128 Helen Diller Family Cancer Research Building 1450 3rd Street, HD555 San Francisco, CA 94158-9001 Tel: (415) 514-1530 Fax: (415) 502-3179 Email: tokuyasu@cc.ucsf.edu [[alternative HTML version deleted]]

Thanks alot for the reply, Christian. ROOT and xps are cool, good luck with it. _Taku -----Original Message----- From: cstrato [mailto:cstrato@aon.at] Sent: Fri 11/20/2009 8:14 AM To: Tokuyasu, Taku Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] xps - hugene 1.0 st quality assessment? Dear Taku, Currently pseudo images, NUSE, RLE plots are not yet implemented in xps, however these are definitely on my to-do list in the near future. Best 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 _._._._._._._._._._._._._._._._._._ Tokuyasu, Taku wrote: > Is there a standard workflow to produce RMA/PLM chip pseudo images, > NUSE, RLE plots and the like for HuGene 1.0 ST arrays in xps? I think > creating an AffyBatch object may be the way to go, but I'd like to > confirm this first before figuring out how to create one. Will this run > into memory issues? > > > > Regards, > > > > _Taku > > > > Taku A. Tokuyasu, PhD > > Computational Biologist > > Biostatistics and Computational Biology Core > > UCSF, Box 0128 > > Helen Diller Family Cancer Research Building > > 1450 3rd Street, HD555 > > San Francisco, CA 94158-9001 > > Tel: (415) 514-1530 > > Fax: (415) 502-3179 > > Email: tokuyasu at cc.ucsf.edu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >

Dear Taku, Currently pseudo images, NUSE, RLE plots are not yet implemented in xps, however these are definitely on my to-do list in the near future. Best 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 _._._._._._._._._._._._._._._._._._ Tokuyasu, Taku wrote: > Is there a standard workflow to produce RMA/PLM chip pseudo images, > NUSE, RLE plots and the like for HuGene 1.0 ST arrays in xps? I think > creating an AffyBatch object may be the way to go, but I'd like to > confirm this first before figuring out how to create one. Will this run > into memory issues? > > > > Regards, > > > > _Taku > > > > Taku A. Tokuyasu, PhD > > Computational Biologist > > Biostatistics and Computational Biology Core > > UCSF, Box 0128 > > Helen Diller Family Cancer Research Building > > 1450 3rd Street, HD555 > > San Francisco, CA 94158-9001 > > Tel: (415) 514-1530 > > Fax: (415) 502-3179 > > Email: tokuyasu at cc.ucsf.edu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >