Hi Shirley The multidensity and multiecdf functions in the geneplotter package are also attempts to address your use case. Let me know how you find them. Best wishes Wolfgang -- ---------------------------------------------------- Wolfgang Huber EMBL-EBI http://www.ebi.ac.uk/huber julien laffaire wrote: > Perhaps you should do it like this : > > v1, v2 and v3 are 3 vectors of inequal sizes. > > plot(density(v1), xlim=c(), ylim=c(), col="black") > lines(density(v2), col="red") > lines(density(v3), col="blue") > > In this way you don't have to add NA values but you will need to "play" with xlim and ylim to find the good scale. > > is it ok ? > J > > --- En date de : Mar 10.2.09, shirley zhang <shirley0818 at="" gmail.com=""> a ?crit : > >> De: shirley zhang <shirley0818 at="" gmail.com=""> >> Objet: Re: Re : [BioC] missing value in plotDensity >> ?: roomjr at yahoo.fr >> Cc: "Bioconductor Mailing List" <bioconductor at="" stat.math.ethz.ch=""> >> Date: Mardi 10 F?vrier 2009, 14h57 >> 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 >>>> >>>> _______________________________________________

Hi, plotDensity() of aroma.light takes either a (i) vector, (ii) matrix, (iii) data.frame, or a (iv) list of vectors. Examples: v1 <- rnorm(1000); v1[200:300] <- NA; v2 <- rnorm(500); v3 <- rnorm(600); v1[100:300] <- NA; aroma.light::plotDensity(list(v1,v2,v3)); See help("plotDensity.list", package="aroma.light") for more details. /Henrik On Tue, Feb 10, 2009 at 6:40 AM, julien laffaire <roomjr at="" yahoo.fr=""> wrote: > Perhaps you should do it like this : > > v1, v2 and v3 are 3 vectors of inequal sizes. > > plot(density(v1), xlim=c(), ylim=c(), col="black") > lines(density(v2), col="red") > lines(density(v3), col="blue") > > In this way you don't have to add NA values but you will need to "play" with xlim and ylim to find the good scale. > > is it ok ? > J > > --- En date de : Mar 10.2.09, shirley zhang <shirley0818 at="" gmail.com=""> a ?crit : > >> De: shirley zhang <shirley0818 at="" gmail.com=""> >> Objet: Re: Re : [BioC] missing value in plotDensity >> ?: roomjr at yahoo.fr >> Cc: "Bioconductor Mailing List" <bioconductor at="" stat.math.ethz.ch=""> >> Date: Mardi 10 F?vrier 2009, 14h57 >> 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 > >> http://fr.docs.yahoo.com/mail/transfert_mails.html >> > > > > _______________________________________________________________ ___________________________________ > Ne pleurez pas si votre Webmail > hoo.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 >