[BioC] arrayQualityMetrics is not working

[Steve Lianoglou]

Hi,

On Mon, Feb 14, 2011 at 5:09 AM,  <nqueralt at clinic.ub.es> wrote:
> Dear all,
>
> I'm trying to run the arrayQualityMetrics function for the first time and an error comes out:
>
>> arrayQualityMetrics(RG, outdir="QCMetrics_onRG/", force=TRUE, do.logtransform=TRUE)
>
> The directory 'QCMetrics_onRG/' has been created.
>
> KernSmooth 2.23 loaded
>
> Copyright M. P. Wand 1997-2009
>
> (loaded the KernSmooth namespace)
>
> [[1]]
>
>
>
> Error en aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
>
>  no se pudo encontrar la función "svg"

My spanish is a bit rusty, but it looks like this is your problem.

For some reason the "svg" function is not there, and I believe that it
should be (I'm no R windows expert, though).

Can you copy/paste the result you get when you call  capabilities()
from the R prompt. Eg. I get:

R> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
    TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE
  libxml     fifo   cledit    iconv      NLS  profmem    cairo
    TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE

And I believe having the "cairo" value == TRUE is essential to have svg working.

Maybe you need to install the "Cairo" library?

http://cran.r-project.org/web/packages/Cairo/index.html

Don't know ... not exactly sure.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact