[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
> 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.
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