Dear List, I had posted earlier about my problem but didn't get any response that could help so I am seeking your help again. I have duplicate spots on my nimblegen array that are position randomized so there is no order to their placement. In Limma when we call the duplicateCorrelation() function, it requires that the duplicate spots have some order to them, like they are either adjacent or they are on upper and lower halves of the array. In this case, can someone please help me about how to go about analyzing these spots? I really appreciate your input. Sincerely, Vishal Code: corfit=duplicateCorrelation(ma.quantile, ndups=2) This gives me a negative corelation of -0.08 the reason being that the spots are randomized. Is there a solution to this? [[alternative HTML version deleted]]

I always sort by probename, which makes the spots adjacent in the data matrix. )f course, this destroys the spatial correlation, so if you plan to do some spatial adjustment, you should do it first. --Naomi At 01:45 PM 5/5/2009, Vishal Thapar wrote: >Dear List, > >I had posted earlier about my problem but didn't get any response that could >help so I am seeking your help again. > >I have duplicate spots on my nimblegen array that are position randomized so >there is no order to their placement. In Limma when we call the >duplicateCorrelation() function, it requires that the duplicate spots have >some order to them, like they are either adjacent or they are on upper and >lower halves of the array. In this case, can someone please help me about >how to go about analyzing these spots? > >I really appreciate your input. > >Sincerely, > >Vishal > >Code: > >corfit=duplicateCorrelation(ma.quantile, ndups=2) > >This gives me a negative corelation of -0.08 the reason being that the spots >are randomized. Is there a solution to this? > > [[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

Hi Vishal, One way to do this is to use the probe IDs as names of your data points. I don't know how your system is set up, but I'll show how I summarize by name without changing the original order of the spots: mywtfun <- function(exclude.flags=c(1,2,3,4,5,6,7)) function(obj) 1-(obj$Flag %in% exclude.flags) RG.MDA <- read.maimages(file.MDA, source="imagene", names=target.MDA$Barcode, wt.fun=mywtfun(c(1,2,3,4,5,6,7)), columns=list(f="Signal Mean",b="Background Median")) rownames(RG.MDA) <- RG.MDA$genes[,6] Cy3.channel.MDA = RG.MDA$G expression.matrix.MDA <- apply(Cy3.channel.MDA,2,function(v){tapply(v,names(v), function(x){median(x,na.rm=TRUE)})}) I use the median of the replicated spot rather than the mean. I hope it can be of some use and that Outlook doesn't break my lines in silly places. Good luck Peder Best regards Exiqon A/S Peder Worning, Ph.D. Senior Scientist, Biomarker Discovery Telephone: +45 45650457 Telefax: +45 45661888 E-mail: pwo at exiqon.com Bygstubben 3 DK-2950 Vedbaek Denmark www.exiqon.com The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Vishal Thapar Sent: Tuesday, May 05, 2009 7:45 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] random positioning of duplicate spots Dear List, I had posted earlier about my problem but didn't get any response that could help so I am seeking your help again. I have duplicate spots on my nimblegen array that are position randomized so there is no order to their placement. In Limma when we call the duplicateCorrelation() function, it requires that the duplicate spots have some order to them, like they are either adjacent or they are on upper and lower halves of the array. In this case, can someone please help me about how to go about analyzing these spots? I really appreciate your input. Sincerely, Vishal Code: corfit=duplicateCorrelation(ma.quantile, ndups=2) This gives me a negative corelation of -0.08 the reason being that the spots are randomized. Is there a solution to this? [[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