[BioC] assign a same probe to differents probesets

lgautier at altern.org lgautier at altern.org
Mon Sep 17 22:31:06 CEST 2007

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
- 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..


> 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
> probeset, one probe (named P) has the same coordinate than in the first
> 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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