[BioC] how to use R read CHP file

Ben Bolstad bmb at bmbolstad.com
Sun Dec 11 19:47:16 CET 2005

Actually the CHP files are files containing pre-processed results eg 
MAS 5.0 or similar from MAS or GCOS. They are not the same as CDF files.
As far as I know there is no current functionality for reading CHP files
into BioConductor. 

Instead the recommended procedure is as Kasper recommends. Get hold of
the CEL files for your data, if possible. Then read them using the
routines in the affy package. Consider pre-processing your data using
rma() or gcrma().

Hope that helps,


On Sun, 2005-12-11 at 09:31 -0800, Kasper Daniel Hansen wrote:
> 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.
> Kasper
> 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
> >
Ben Bolstad <bmb at bmbolstad.com>

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