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[netCDF #SCH-450091]: GWASTools & Affymetrix

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:


or from one of the binary Windows distributions available here:



> ---------------------------------------------
> Silvano Cesar da Costa
> Universidade Estadual de Londrina
> Centro de CiÃncias Exatas
> Departamento de EstatÃstica
> 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

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