Our slide design had some spots were duplicated and some were not. I am using limmaGUI, but duplicated spots were recognized by space between spots. How can I handle the spots that were not duplicated? Should add flags in spottype file and exclude those? Is there any way to combine duplicated spots by ID or name in Limma? Thank you. Wonjong. Bioinformatician SBRI.

Hi, You can combine duplicate spots by ID with a script similar like this (assuming that your duplicated clones have a smaller ID than the ones that are not duplicated): index <- order(MA$genes$ID) MAsorted <- MA[index,] MAsorted$printer$spacing <- 1 And then average the clones in the subset of the MAList where you have duplicated clones. Let say that your duplicated clones have an ID below 200000: Subset <- MAsorted$genes$ID < 200000 MAsubset <- MA[Subset,] If your clones that are duplicated have not a smaller ID than the ones that are not duplicated, you can make an extra column in your MAList where you can put a dummy ID where this is true. Best regards Jo?o Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: Joao.Fadista at agrsci.dk Web: http://www.agrsci.org This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Wonjong Moon Sent: Thursday, April 19, 2007 2:46 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Duplicated spots in limmaGUI Our slide design had some spots were duplicated and some were not. I am using limmaGUI, but duplicated spots were recognized by space between spots. How can I handle the spots that were not duplicated? Should add flags in spottype file and exclude those? Is there any way to combine duplicated spots by ID or name in Limma? Thank you. Wonjong. Bioinformatician SBRI. _______________________________________________ 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