Hi Wyatt, Mcmahon, Wyatt wrote: > Thank you very much, Naomi! > > When you say, "sort by gene so that the duplicates are adjacent in the > data matrix," do you mean by using Excel? That's a joke, right? If not, you need to sit down and read 'An Introduction to R'. Right now. Really. You could sort using Excel, but that would be like using the butt-end of a screwdriver to pound a nail when you have a hammer hanging on your belt. You could do it, and eventually you would get the job done, but you are really using the wrong tool for the job. Best, Jim > > Thanks, > > Wyatt > > -----Original Message----- > From: Naomi Altman [mailto:naomi at stat.psu.edu] > Sent: Thursday, June 07, 2007 3:36 PM > To: Mcmahon, Wyatt; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Agilent's duplicate spots > > I think most of us have found that the spatial aspect is not that > important. Normalize the data and then sort by gene so that the > duplicates are adjacent in the data matrix. > > --Naomi > > At 02:16 PM 6/7/2007, Mcmahon, Wyatt wrote: > >>Hello everyone, >> >> >> >>I'm new to bioconductor and microarray in general, so please excuse my >>ignorance. >> >> >> >>I am trying to analyze my microarray experiment using limma. We have >>used Agilent to spot our arrays, and we have duplicate spots. However, >>these spots are placed randomly over the entire chip. How do I let >>limma know that there are duplicate spots with a random distribution. > > I > >>can't seem to find anything that explains this. >> >> >> >>Thanks in advance, >> >> >> >>Wyatt >> >> >> >>K. Wyatt McMahon, Ph.D. >> >>Postdoctoral Research Associate - Functional Genomics Center and >>Services Facility >> >>Texas Tech University >> >>Department of Plant and Soil Sciences >> >>Campus Box 42122 >> >>79409 >> >>806-742-5073 ext. 263 >> >> >> >> >> [[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 > > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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.