[BioC] Missing probesets

[Robert Gentleman]

On May 2, 2005, at 12:16 AM, Malick.PAYE at eu.biomerieux.com wrote:

>
>
> Hello all,
>
> I installed Bioconductor, the affy package as well as the makecdfenv
> package.
> I have some problems with package makecdfenv (make.cdf.package  
> function).
>
> I'm working with a custom chip, then I tried to create a CDF package  
> using
> my CDF file, when creating and installing the package everything seems  
> to
> be ok but when i read my cel files I realise that about 20% of my
> probesets are missing.
>
> While trying to track the bug it seems that the missing probesets are
> those whose probes are completely/partially included in another  
> probeset ?
>

  Hi,
    I am not sure I understand what you are saying here. Are you saying  
that some probes on your chip map to multiple mRNA's? That does seem a  
bit peculiar and it will not be precisely clear how to analyze such  
data. I suspect that some form of very large EM iteration will be  
needed, but I would not expect anything to do it correctly off of the  
shelf.
    If this supposition is correct you now need to deal explicitly with  
cross-hybridization - how much of the signal at each such probe do you  
attribute to the *different* underlying mRNA species. This is doable,  
provided there is no complete confounding - or stated differently  
provided each mRNA species has at least one probe that is unique to it  
[probably - there are sure to be more specific conditions since this is  
going to become a large optimization problem] - but it is not simple to  
do.

   Duplicating the probes, to give the appearance of every gene having a  
complete probe set will bias your results [directions unknown] and  
probably should not be used - unless you have no other choices.


  Best wishes,
     Robert
> So I suppose that the implementation of this package prevents the
> inclusion of a probeset in another ?
>
> My question : what can I do to reanalyse my data with the entire
> probesets.
>
> I'm not familiar with C language so I can't have a look at the source
> code.
>
> PS : I'm using R version 2.0.1, affy version 1.5.8-1 and Makecdfenv :
> version: 1.4.8
>
> If someone met this kind of problem. ..
>
> Any help would be greatly appreciate.
>
> Malick,
>
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+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
                          |
+----------------------------------------------------------------------- 
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+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
                          |
+----------------------------------------------------------------------- 
----------------+