[BioC] analyze HuEx array using HuGene .cdf file

[shirley zhang]

Hi Mark,

Thanks for you suggestion. Actually I just got the mapping file from
Affy. If anybody in this list needs this file, you can contact Affy or
me.

I appreciate all of your help,
Shirey

On Wed, Dec 17, 2008 at 6:08 PM, Mark Robinson <mrobinson at wehi.edu.au> wrote:
> 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
> ------------------------------
>
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>