[BioC] analyze HuEx array using HuGene .cdf file

[Kasper Daniel Hansen]

Please re-read Laurents reply.

The problem is that even thought he same probe(set) may be present on  
the two arrays, the (x,y) location (spatial) of the probe is most  
likely not the same. So you will need to remap everything in a spatial  
way.

Yes, that can be done using R and following some of the things in the  
post Jenny linked to + some custom code to take care of the spatial re- 
organization. But it will require that you familiarize yourself with  
the underlying data structures and it won't be a 1-2 hour exercise  
(unless you really know your way around these data structures).

Kasper

On Dec 11, 2008, at 14:01 , shirley zhang wrote:

> Hi Larurent,
>
> Thanks for your quick reply.  You are right, CDF file also includes
> the location of probes on the chip. In that case, can I modify the
> HuEx .cdf file to mask those probes not found in Hugene array as
> NA/missing, and then use this modified .cdf file to analyze exon
> array? If can, do you know how to do it in R or other tools?
>
> Thanks a lot,
> Xiaoling
>
>
>
>
> On Thu, Dec 11, 2008 at 10:40 PM, Laurent Gautier  
> <laurent at cbs.dtu.dk> wrote:
>> shirley zhang wrote:
>>>
>>> Dear List,
>>>
>>> I have a quick question. Since the HuGene probes are largely a  
>>> subset
>>> of the HuEx probes, we would like to use that subset of probes for  
>>> the
>>> HuEx array, then compare the results with that of using HuEx's own
>>> core probes which we already have. For this purpose,  can I use
>>> HuGen's .cdf file to analyze HuEx arrays?
>>
>> I'd say that you mostly likely can't.
>>
>> The CDF definition contains information relative to the relative  
>> spatial
>> location of the features (probes) on the chip, and unless the  
>> HuGene is a
>> subset also in the spatial sense of it (that is  "like HuEx but  
>> with probes
>> missing from their location on the array").
>>
>>> If not, how to
>>> generate/modify a .cdf file based on HuGen probes to analyze HuEx
>>> array data?
>>
>> HuGen(e{0,1}), HuEx, or else, you should have the corresponding .cdf
>> distributed with the arrays (and you'll contact Affymetrix if this  
>> is not
>> the case).
>>
>>
>> L.
>>
>>> Thanks,
>>> Shirley
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>>
>
> _______________________________________________
> 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