[BioC] analyze HuEx array using HuGene .cdf file

[Mark Robinson]

Shirley.

I don't think you'll find a probe id to probe id mapping.  I think the  
way to go is take the probe *sequences* from HuEx and match them to  
the sequences on HuGene.

At that link you sent below, there is a section called 'Sequence  
Files' and there is a 'probe.tab' file that you can download (you can  
get a corresponding file for HuGene).  Use this to create the set of  
HuEx probes that are represented on HuGene ... and then do your thing  
with removing stuff from the CDF.

Hope that helps.

Cheers,
Mark


On 18/12/2008, at 8:24 AM, shirley zhang wrote:

> Hi All,
>
> Thanks for all of your help.
>
> Since we already have 80 HuEx chips data, we want to
> reanalyze these HuEx data by only looking at those probes on HuGen
> array, then to see whether we get similar results as before. If the
> result is consistent, we are happy to switch the platform in our other
> studies.  In order to find the matched probes between HuEx and HuGene,
> I looked at  the data that has already been generated at Affymetrix
> that compares the probes from the Exon array with the Gene array at
>
> http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st 
> .
>
> This kind of data is exactly what I want. However, those comparison
> files, for example "Human Exon 1.0 ST to Human Gene 1.0 ST, Best Match
> (zip, 485 KB)" only includes the best matched probeset Ids between
> HuEx and HuGene.  Where can I get the matched probe Id between  these
> two platforms? If I can get the matched probe Ids, I can modify HuEx
> CDF file in the way that masking those probes not found in Hugene
> array as NA/missing, and then use this modified .cdf file to analyze
> exon array.
>
> Thanks again,
> Xiaoling
>
> On Fri, Dec 12, 2008 at 5:33 AM, Henrik Bengtsson <hb at stat.berkeley.edu 
> > wrote:
>> Hi,
>>
>> to second what already have been said and explained; you cannot reuse
>> that CDF for a different chip type.  The chip types doesn't even have
>> the same number of probes.
>>
>> Note that:
>>
>> Robinson, M. D. & Speed, T. P. A comparison of Affymetrix gene
>> expression arrays. BMC Bioinformatics, 2007, 8, 449. URL:
>> http://www.biomedcentral.com/1471-2105/8/449/abstract/
>>
>> did this kind of comparison across these chip types.   Mark Robinson
>> used aroma.affymetrix for this.  I'm sure he reads this thread so I
>> can correct me if I'm wrong.  He and Elizabeth Purdom (I think)
>> created custom CDFs for this, cf.
>>
>> http://groups.google.com/group/aroma-affymetrix/web/huex-1-0-st-v2
>>
>> Hope this helps
>>
>> Henrik
>>
>>
>>
>> On Thu, Dec 11, 2008 at 6:02 AM, shirley zhang  
>> <shirley0818 at gmail.com> 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? If not, how to
>>> generate/modify a .cdf file based on HuGen probes to analyze HuEx
>>> array data?
>>>
>>> Thanks,
>>> Shirley
>>>
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>>
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852