Thanks for your prompt reply.

B. Bolstad  wrote :
It is not really ReadAffy() that is having problems since it doesn't
care much at all about the mapping between probes and probesets. 

Since I don't work with non-standard data like this, I don't guarantee
any particular great insights to this situation. But at a guess I'd say
it is a problem in one of these two situations:

1) The creation of the cdfenv
2) How data is extracted from the AffyBatch using the cdfenv

In the case of 1) it may be that the text CDF parser (I assume that this
is the format you are using for your CDF file), does not allow multiple
mappings when it builds the cdfenv. Supposing you actually have this
CDFenv with only two probesets, you could actually see how it is mapping
probes to probesets using

I looked at the read.cdf code. A matrix is built which contains for each 
probe coordinate, the corresponding probeset (and only one). So, when the 
cdf file is parsed, if a probe is assigned to 2 probesets, only the second 
one is kept. (the first one is overwrote)
So the problem is actually that the CDF parser does not allow multiple 
mappings.

Thanks all,

Maud

 


Maud ARSAC | bioMérieux | BioMathematician, IT 
Phone: +33 (0)4 78 87 24 94 | Fax: +33 (0)4 78 87 75 90 
[ 376 Chemin de l'Orme ,   69280  Marcy l'Etoile ] 





lgautier@altern.org
17/09/2007 22:31

 
        Pour :  Maud.ARSAC@eu.biomerieux.com
        cc :    bioconductor@stat.math.ethz.ch, bmb@bmbolstad.com
        Objet : Re: [BioC] assign a same probe to differents probesets


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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