Hi Jenny, I have never needed to use the subset argument, so don't know for sure. However, the subsetting appears to be done at the C level rather than at the R level, so I would bet there isn't much copying being done, which is the only way I know that more memory would be required. My bet is that it would take less memory. Ben Bolstad would know for sure, since he wrote the C code. Best, Jim Jenny Drnevich wrote: > Hi Jim, > > Do you know if using the 'subset' argument of rma() has any effect on the > memory it uses? I'm not sure if it would decrease the memory requirements > by working with less data, or actually increase it by doing a subsetting > step somewhere. > > Thanks, > Jenny > > At 07:37 AM 9/9/2006, James W. MacDonald wrote: > >>Dana Wohlbach wrote: >> >>>Does anyone know of a way to exclude individual probes before >>>normalizing using a method like RMA? In other words, I have >>>identified certain probes in my CEL files that I don't want included >>>in the normalization procedure. Is there a way to use Bioconductor >>>to make this happen? >> >>See ?rma(), in particular the 'subset' argument. >> >>Best, >> >>Jim >> >> >> >>>Thanks, >>>Dana >>> >>>_______________________________________________ >>>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 >> >> >>-- >>James W. MacDonald >>University of Michigan >>Affymetrix and cDNA Microarray Core >>1500 E Medical Center Drive >>Ann Arbor MI 48109 >>734-647-5623 >> >> >> >>********************************************************** >>Electronic Mail is not secure, may not be read every day, and should not >>be used for urgent or sensitive issues. >> >>_______________________________________________ >>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 > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.