[BioC] how to use R read CHP file

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Sun Dec 11 20:25:02 CET 2005

I got a private email worded in such a way that I think Zhidong means  
cel/cdf files when (s)he talks about chp files. I could be wrong.  
Anyway, as Ben said, the chp files are not that interesting.


On Dec 11, 2005, at 10:47 AM, Ben Bolstad wrote:

> 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,
> Ben
> 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>
> http://bmbolstad.com

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