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[netCDF #SCH-450091]: GWASTools & Affymetrix

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  • Subject: [netCDF #SCH-450091]: GWASTools & Affymetrix
  • Date: Wed, 22 Aug 2012 16:20:55 -0600
Hi Silvano,

> I'm trying to use GWASTools (software R) with data provided by Affymetrix.
> 
> I want to read intensity data.
> 
> The command GWASTools is provided by:
> 
> file <- system.file ("extdata", "affy_qxy.nc" package = "GWASdata")
> nc <- NcdfIntensityReader (file)
> 
> where file receives data affy_qxy_nc, the subdirectory extdata, GWASdata
> package.
> 
> The question is: which variables are presents in affy_qxy_nc and how to
> obtain them from the archives of Affymetrix?

I'm guessing you need to use the "ncdump" command-line tool with option "-c", 
as in:

  ncdump -c affy_qxy.nc

to show you all the variables, along with their types, shape, and attributes.

You can get ncdump if you install netCDF from source:

  http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_2_1_1/

or from one of the binary Windows distributions available here:

  http://www.unidata.ucar.edu/software/netcdf/win_netcdf/

--Russ

> ---------------------------------------------
> Silvano Cesar da Costa
> 
> Universidade Estadual de Londrina
> Centro de Ciências Exatas
> Departamento de Estatística
> 
> Fone: (43) 3371-4346
> ---------------------------------------------
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: SCH-450091
Department: Support netCDF
Priority: Normal
Status: Closed