[BioC] Re : missing value in plotDensity

[Jenny Drnevich]

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 écrit :
> >
> >> De: shirley zhang <shirley0818 at gmail.com>
> >> Objet: [BioC] missing value in plotDensity
> >> À: "Bioconductor Mailing List" <bioconductor at stat.math.ethz.ch>
> >> Date: Lundi 9 Février 2009, 22h14
> >> Hi All,
> >>
> >> Does anybody know how to use plotDensity() with missing
> >> value?
> >>
> >> Thanks,
> >> Shirley
> >>
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> >
> >
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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.
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e-mail: drnevich at illinois.edu