[BioC] [Now off-topic] Chromosome view of Nimblegen data

Sean Davis sdavis2 at mail.nih.gov
Fri Dec 15 15:17:33 CET 2006

On Friday 15 December 2006 05:51, J.delasHeras at ed.ac.uk wrote:
> Quoting Sean Davis <sdavis2 at mail.nih.gov>:
> > On Thursday 14 December 2006 14:43, Rustici, Gabriella (NIH/NCI) [F] 
> >> Hi all,
> >> Is there a Bioconductor package I could use to visualize Nimblegen
> >> ChIP-chip data?
> >> I'd like to do a whole genome plot showing chromosome location of
> >> enriched genes for the TF of interest.
> >> Could I use "geneplotter" to do it?
> >
> > You probably could.  However, you might want to look into using the
> > Affymetrix
> > Integrated Genome Browser (IGB) for visualizing your ChIP/chip data.  It
> > takes as input simple text files for visualization purposes.  It is a
> > Java program, so runs fine on windows, linux, and Macos.
> >
> > As an aside, I have an R package for chip/chip analysis that is available
> > here:
> >
> > http://watson.nci.nih.gov/twiki/bin/view/Main/MeltzerLabSoftware
> >
> > It includes functionality to load the nimblegen GFF files, calculate some
> > stats for each probe, and then export the results and raw data for
> > viewing in the Affy IGB.  It is still very much under development, so I
> > would appreciate any feedback if you decide to use it.
> >
> > Sean
> Hi Sean,
> as I have Nimblegen data too, I got very happy to see this :-)
> However I cannot even get the package to load and I am wondering if at
> the moment you can only run it on a Mac? I'm running WinXP.
> I downloaded the .gz file, and uncompressed it with 7zip. The
> resulting .tar file is nothing that I seem to be able to deal with
> from the RGui menu, so I uncompressed it again to give a folder called
> 'chIPchip', containing sevral other folders. Then I compressed it into
> a .zip file, and tried to install it from the menu (install package
> from local zip files). That proceeds without errors, but then:
> > library(chIPchip)
> Error in library(chIPchip) : 'chIPchip' is not a valid package --
> installed < 2.0.0?
> I am sure you're laughing at my naivety thinking that this roundabout
> would work, but I just don't know what else I could do, other than
> getting a Mac? :)
> Is there any way to install the package to run on a WinXP system?

I'm sorry to clutter the list with non-bioc related issues, but I 
inadvertently opened a can of worms yesterday in this thread.

The package is a SOURCE package, so, unfortunately, you need to have tools to 
build the package from source.  These are standard on Mac, Linux, and Unix, 
but of course are NOT on Windows.  So, to get the software running, you will 
need to enable your computer to build packages from source or use a computer 
with another OS.  When this gets moved over to bioconductor, this will no 
longer be an issue.


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