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 The information transmitted in this electronic communication...{{dropped}}

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. Kasper 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 > > > > > > > The information transmitted in this electronic communication... > {{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

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