Hi Xiaoling, Julien's advice worked for me, so how is it not working for you? You should post your code that is not working, along with the output of sessionInfo() as per the posting guide. Here's my code that worked: > x <- matrix(rnorm(15000,mean=6),ncol=3) > dim(x) [1] 5000 3 > x[1:500,1] <- NA > x[501:1000,2] <- NA > x[4501:5000,3] <- NA > plotDensity(x) > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] affyQCReport_1.20.0 geneplotter_1.20.0 lattice_0.17-15 [4] RColorBrewer_1.0-2 simpleaffy_2.18.0 made4_1.16.0 [7] ade4_1.4-9 affyPLM_1.18.0 preprocessCore_1.4.0 [10] affycoretools_1.14.0 annaffy_1.14.0 KEGG.db_2.2.5 [13] gcrma_2.14.1 matchprobes_1.14.0 biomaRt_1.16.0 [16] GOstats_2.8.0 Category_2.8.1 genefilter_1.22.0 [19] survival_2.34-1 RBGL_1.18.0 annotate_1.20.1 [22] xtable_1.5-4 GO.db_2.2.5 RSQLite_0.7-1 [25] DBI_0.2-4 AnnotationDbi_1.4.1 graph_1.20.0 [28] limma_2.16.3 affy_1.20.0 Biobase_2.2.1 [31] RWinEdt_1.8-0 loaded via a namespace (and not attached): [1] affyio_1.10.1 cluster_1.11.11 grid_2.8.0 GSEABase_1.4.0 [5] KernSmooth_2.22-22 RCurl_0.91-0 XML_1.94-0.1 > Cheers, Jenny At 07:57 AM 2/10/2009, shirley zhang wrote: >Hi Julien and Bioconductor > >Thanks for your reply and sorry that I did not make myself clear. > >I would like to draw 3 density plots in one figure. Since the size of >each vector is different, I created a matrix "x" by adding NA value in >order to make the size same. However when I call plotDensity(x) in >package "affy", it gives me the following error message: > >"x contains missing values". > >My problem is how to draw 3 density plots in one figure when the size >is different. > >Thanks, >Xiaoling > >On Mon, Feb 9, 2009 at 4:57 PM, julien laffaire <roomjr at="" yahoo.fr=""> wrote: > > Hi Shirley, > > you can handle missing values with the na.rm > option which is TRUE by default. I've change > some values of one of my dataset to NA et it works well. > > I hope it can help. > > Julien > > > > > > > > --- En date de : Lun 9.2.09, shirley zhang > <shirley0818 at="" gmail.com=""> a ?crit : > > > >> De: shirley zhang <shirley0818 at="" gmail.com=""> > >> Objet: [BioC] missing value in plotDensity > >> ?: "Bioconductor Mailing List" <bioconductor at="" stat.math.ethz.ch=""> > >> Date: Lundi 9 F?vrier 2009, 22h14 > >> Hi All, > >> > >> Does anybody know how to use plotDensity() with missing > >> value? > >> > >> Thanks, > >> Shirley > >> > >> _______________________________________________ > >> 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 > > > > > > > ____________________________________________________________________ ______________________________ > > Ne pleurez pas si votre Webmail ferme ! > R?cup?rez votre historique sur Yahoo! Mail ! > http://fr.docs.yahoo.com/mail/transfert_mails.html > > > >_______________________________________________ >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