[BioC] Chromosome view of Nimblegen data
J.delasHeras at ed.ac.uk
J.delasHeras at ed.ac.uk
Fri Dec 15 11:51:01 CET 2006
Quoting Sean Davis <sdavis2 at mail.nih.gov>:
> On Thursday 14 December 2006 14:43, Rustici, Gabriella (NIH/NCI) [F] wrote:
>> 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
> 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
> 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.
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:
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?
R version 2.4.0 (2006-10-03)
attached base packages:
 "methods" "stats" "graphics" "grDevices" "utils" "datasets"
other attached packages:
Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
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