[BioC] how to use R read CHP file

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Sun Dec 11 18:31:28 CET 2005

Hi Zhidong

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/ 
annotation/stable/src/contrib/html/ )

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  
cel files
but I would recommend that you stick to the affy package if you are a  
"new" user.


On Dec 11, 2005, at 2:22 AM, zhu zhidong wrote:

>  Hi,
>  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
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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