[BioC] problem in diagnostic plots?
Robert Gentleman
rgentlem@jimmy.harvard.edu
Wed, 31 Jul 2002 10:57:15 -0400
On Wed, Jul 31, 2002 at 07:19:10PM +1000, Peter Baker (CMIS, Indooroopilly) wrote:
> Hi All
>
> I've just started using Bioconductor and seems really good.
>
> As a test, I've read in two GenePix files - essentially the same code
> as ReadSpot example and seem to be able to plot, print, normalise ....
>
> The only problem I've encountered is
>
> > maDiagnPlots1(test[,2])
> Error in plot.new() : Figure margins too large
> > maRawPlots(test[,2])
> Error in plot.new() : Figure margins too large
> > maNormPlots(test[,2])
> Error in maMloc(structure(list(), maRf = structure(c(4109, 771, 3073, :
> No direct or inherited method for function "maMloc" for this call
>
Hi,
We have had at least one similar report. I am not sure what the
problem is precisely. Perhaps the names for the axis labels or some
text is too long. We will have a look and see if we can sort out
what the problem is.
Robert
> I get the first plot only - seems to stop at the second
>
> Does anyone recognise this sort of problem?
>
> Could it be missing values? Do I need to filter these in some way
> before plotting? The arrays have row 10 of each 'block' empty
>
> ------------------------------------------------
>
> However, plots like these work absolutely fine
>
> ### backgrounds
> maImage(test[,1], x = "maGb", contour=TRUE)
> maImage(test[,1], x = "maRb", contour=TRUE)
>
> ### raw images
> maImage(test[,1])
>
> > version
> _
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 1
> minor 5.1
> year 2002
> month 06
> day 17
> language R
>
> > Sys.info()
> sysname release
> "Linux" "2.4.18-5smp"
> (RedHat linux 7.3)
>
> Thanks for your help
>
> Regards
> Peter
>
>
> --
> Dr Peter Baker, Statistician (Bioinformatics/Genetics),
> CSIRO Mathematical & Information Sciences,
> 120 Meiers Rd, INDOOROOPILLY, QLD 4068. Australia.
> Email: <Peter.Baker@csiro.au>
> WWW: http://www.cmis.csiro.au/Peter.Baker/
> Phone:+61 7 3214 2210 Fax:+61 7 3214 2881
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
+---------------------------------------------------------------------------+
| Robert Gentleman phone : (617) 632-5250 |
| Associate Professor fax: (617) 632-2444 |
| Department of Biostatistics office: M1B20
| Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu |
+---------------------------------------------------------------------------+