[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   
> 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?



> sessionInfo()
R version 2.4.0 (2006-10-03)

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United  
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

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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