Dear all, As read from the instruction of backgroundCorrect in limma, the method "half", "minimum", "edwards" and so on are all designed to produce positive corrected intensities. My code is as follows: rgc<-backgroundCorrect(rg, method="half") plotDensities(rgc) After I plot the graph of Density-Intensity after this backgroud correction, I found there is still some part of curve with the negative intensity. Why is it like that?? I try minimun also, the result is similar with negative intensity. I dont know how to explain it. Expecting your reply. Regards, Yanju

Hi Yanju, 'plotDensities' plots the log2 of the R and G values, and log2 values of positive values less than 1 are negative. Jenny At 09:06 AM 11/28/2006, yanju wrote: >Dear all, > >As read from the instruction of backgroundCorrect in limma, the method >"half", "minimum", "edwards" and so on are all designed to produce >positive corrected intensities. My code is as follows: > > rgc<-backgroundCorrect(rg, method="half") > plotDensities(rgc) > >After I plot the graph of Density-Intensity after this backgroud >correction, I found there is still some part of curve with the negative >intensity. Why is it like that?? I try minimun also, the result is >similar with negative intensity. I dont know how to explain it. >Expecting your reply. > >Regards, >Yanju > >_______________________________________________ >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