[BioC] analyze HuEx array using HuGene .cdf file

Wolfgang Huber huber at ebi.ac.uk
Thu Dec 11 23:47:50 CET 2008


and the "combineAffyBatch" function in the matchprobes package might be 
somewhat helpful (see package vignette), but as Kasper says, this is not 
something you should do before getting an understanding of how AffyBatch 
represents Affymetrix data, and of how it uses cdf and probe packages to 
that end (see vignette "Primer" of the affy package and in particular 
Section 7 for a start).

Best wishes

Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Kasper Daniel Hansen ha scritto:
> 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

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