The standard way would actually be to use the "affy" package. In that
package you will find the function ReadAffy which is a high-level
function and read.affybatch which is a more low-level function with
better control. Read the help pages, especially the eaxmple.
You may read cdf files using the makecdfenv package, but if you are
using a "standard" affy chip, you can download ready-to-use packages
from Bioconductor (look at http://www.bioconductor.org/packages/data/
You could also use the affxparser package. You can use
read.cel.complete which reads a single cel file (so you need to do
it multiple times and glue it together)
read.cel.intensities which extracts the intensities from multiple
but I would recommend that you stick to the affy package if you are a
On Dec 11, 2005, at 2:22 AM, zhu zhidong wrote:
> I want to use R to extract data from affy .chp file
> I download affxparser package for R, but I can't get help form
> chelp files.
> can you give me an answer.
> zhidong zhu
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch