Hi All I haven't used LIMMA for a while, but I remember that when I did there was a special way to handle duplicate spots. However the layout of the array had to be such that one replicate was printed first for all spots and then the other replicate, because somewhere you had to say something like there are 5000 spots and the next rep starts at spot number 5001. Is this still true? The reason I'm asking is because I'm developing Agilent arrays and they randomize everything so it would not be possible to say the duplicate spots start at a specific place. Thanks Cecilia Cecilia McGregor, Ph.D. Department of Entomology 404 Life Sciences Building Louisiana State University Baton Rouge LA, 70803 USA Office Phone: (225) 578-0518 Lab Phone: (225) 578-0921 Mobile Phone: (225) 763-9138 Fax: (225) 578-1643

Hi Cecila, Yes, this is still true. However, as long as there are the same number of replicate spots per gene, you should be able to fake it. Once you're done with any location-based normalization, you can simply sort your MAlist object so that rows with duplicate spot names are right next to each other. You may have to cut out blanks/control spots/etc. that have a different number of replicates than all of your genes... HTH, Jenny At 03:04 PM 7/23/2008, Cecilia McGregor wrote: >Hi All > >I haven't used LIMMA for a while, but I remember that when I did >there was a special way to handle duplicate spots. However the >layout of the array had to be such that one replicate was printed >first for all spots and then the other replicate, because somewhere >you had to say something like there are 5000 spots and the next rep >starts at spot number 5001. Is this still true? The reason I'm >asking is because I'm developing Agilent arrays and they randomize >everything so it would not be possible to say the duplicate spots >start at a specific place. > >Thanks >Cecilia > >Cecilia McGregor, Ph.D. >Department of Entomology >404 Life Sciences Building >Louisiana State University >Baton Rouge >LA, 70803 >USA > >Office Phone: (225) 578-0518 >Lab Phone: (225) 578-0921 >Mobile Phone: (225) 763-9138 >Fax: (225) 578-1643 > >_______________________________________________ >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 illinois.edu

> I haven't used LIMMA for a while, but I remember that when I did there > was a special way to handle duplicate spots. However the layout of the > array had to be such that one replicate was printed first for all > spots and then the other replicate, because somewhere you had to say > something like there are 5000 spots and the next rep starts at spot > number 5001. You are referring to something like this: dupfit <- duplicateCorrelation(MA, ndups=2, spacing=5000) fit <- lmFit(MA, ndups=2, spacing=5000, correlation=dupfit$consensus) > The reason I'm asking is because I'm developing Agilent arrays and > they randomize everything so it would not be possible to say the > duplicate spots start at a specific place. As long as there is exactly the same number of replicate spots for each probe you could reorder the data beforehand to get consecutive replicate spots - e.g. by Gene ID: MA <- MA[order(MA$genes$ID), ] dupfit <- duplicateCorrelation(MA, ndups=2, spacing=1) fit <- lmFit(MA, ndups=2, spacing=1, correlation=dupfit$consensus) cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel