[BioC] assign a same probe to differents probesets

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Mon Sep 17 22:47:08 CEST 2007

I have experience with such a chip. In my experience - once you have  
the necessary CDF package which can be a pain - there is no problem  
using the standard affy functions. GCRMA however has some problems.

So I guess you are doing something wrong here.


On Sep 17, 2007, at 1:31 PM, lgautier at altern.org wrote:

> Only to second what was stated earlier: ReadAffy has most certainly  
> nothing
> to do with the issue.
> I have some experience with customized CDFs, but I am not certain  
> of what
> you are doing.
> Here is the deal with CDF and CEL files:
> - ReadAffy reads CEL files (and only CEL files) and builds an  
> AffyBatch -
> The relevant CDF mapping structure (currently an R object of type
> "environment") is inferred from the name for the chip type  
> (contained in
> the header of all CEL files. That information (the name) is  
> available in a
> slot of the AffyBatch
> - The default CDF mapping structures are built from CDF files and  
> wrapped
> into packages.
> - There is a package to make the CDF packages mentioned above
> ("makecdfenv").
> - The default CDF mapping structure can be changed by editing the  
> relevant
> slot in the AffyBatch
> Rather than painfully building a "fake" CDF file (and run into
> all sort of trouble with the CDF parsers - you might not know what
> consistency checks are checking), I would recommend to work on  
> building
> directly environments (check the package altcdfenvs)... and if your
> workflow requires you to have data in files, use your own simple file
> format and build the R "environment" from it.
> Regarding the presence of a one probe in several probesets, I would
> think that this is something you want to get rid of..
> Laurent
>> Hi,
>> When a same probe is assigned to 2 or more probesets (in the CDF  
>> file),
> the ReadAffy() function runs oddly.
>> I give you an exemple to explain my problem :
>> I create a CDF file with only 2 probesets of 11 probes (PM). In the
> second
>> probeset, one probe (named P) has the same coordinate than in the  
>> first
> one.
>> Then, when I read some CEL files with this cdf environment in R, the
> second probeset has 11 probes but the first one has only 10  
> probes : the
> intensity of the probe P is missing in the first probeset.
>> I don't understand why the function ReadAffy doesn't manage that  
>> type of
> design ?
>> Do you have any idea about this ?
>> Best regards,
>> Maud
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