[BioC] assign a same probe to differents probesets

Ben Bolstad bmb at bmbolstad.com
Mon Sep 17 16:51:20 CEST 2007


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

as.list(mycdfenv)[1:2]

to confirm that the mapping issue is here. 

In the case of 2) you don't say how you are extracting the data from the
AffyBatch, but I'm assuming you are using something like
pm(my.affybatch). It may be the case that this does situation does not
allow non unique indexing when it goes to extract the data from how it
is stored in the AffyBatch.

Best,

Ben


On Mon, 2007-09-17 at 15:15 +0200, Maud.ARSAC at eu.biomerieux.com wrote:
> 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
> 
> 
> 
> 
> -----------------------------------------------------------------------------
> AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes.
> 
> NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



More information about the Bioconductor mailing list