[BioC] how to make probe environments for use with GCRMA

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Fri Jul 20 23:06:27 CEST 2007

Look at the matchprobes package. Essentially the probe environment is  
a table with three columns: x, y and sequence data (there are a few  
more columns though). So you need some info from you custom array  
about what the probe composition is.


On Jul 20, 2007, at 11:35 AM, Wittner, Ben, Ph.D. wrote:

> I'll be getting data from a custom Affymetrix expression chip and  
> would like to
> use gcrma.
> If the chip is named "foo", in order to use gcrma() I need a foocdf  
> environment
> and a fooprobe environment.
> I've found the package makecdfenv that will allow me to make foocdf  
> given the
> CDF file for the chip.
> Can anyone give me advice for creating the fooprobe environment?
> Thanks very much.
> -Ben
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