[BioC] error with makecdfenv package

[TRAN Trang]

Dear all,

Thank you very much for your suggestion. I  tried the pdInfoBuilder/oligo, it runs very well. 

Best,
Trang

-----Message d'origine-----
De : cstrato [mailto:cstrato at aon.at] 
Envoyé : mercredi 16 juillet 2014 20:07
À : James W. MacDonald; TRAN Trang
Cc : 'bioconductor at r-project.org'
Objet : Re: [BioC] error with makecdfenv package

Dear Jim,

I do not have any plans to support these arrays in the future so oligo would be the only way to go.

Best regards,
Christian


On 7/16/14 7:49 PM, James W. MacDonald wrote:
> Hi Christian,
>
> Thanks! Are there any plans to support these arrays in future, or 
> should I assume that pdInfoBuilder/oligo are the only way to go?
>
> Best,
>
> Jim
>
>
>
> On 7/16/2014 1:39 PM, cstrato wrote:
>> Dear Jim,
>>
>> Please see my response from March:
>> https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html
>>
>> Best regards,
>> Christian
>>
>>
>> On 7/16/14 7:03 PM, James W. MacDonald wrote:
>>> Hi Trang Tran,
>>>
>>> I am redirecting this to the bioconductor help list, so others may 
>>> benefit as well.
>>>
>>> On 7/16/2014 10:22 AM, TRAN Trang wrote:
>>>> Dear all,
>>>>
>>>> I'm using the makecdfenv package to creat a annotation package for 
>>>> the chip Affymetrix  HTA 2.0 from .CDF file but I get the following error:
>>>
>>> You won't be able to use the makecdfenv/affy pipeline for this array.
>>> That pipeline is intended for the old 3'-biased arrays.
>>>
>>> The HTA arrays are very complex, being intended to measure 
>>> transcript splice variants. The pdInfoBuilder/oligo pipeline will 
>>> allow you to read in and summarize the data. I don't know about the 
>>> xps package, but perhaps Christian Stratowa will respond.
>>>
>>> Although you can summarize the data using oligo, there aren't (to my
>>> knowledge) any packages in BioC that are intended to analyze these data.
>>> Note that for each gene there are any number of probesets that are 
>>> intended to measure either exon abundance or to measure the 
>>> existence of an exon-exon junction.
>>>
>>> Summarizing those data into a measure (or measures) that can be used 
>>> to infer differential transcript splicing is probably not a trivial 
>>> exercise. I would be interested to hear if anybody is trying to 
>>> develop a package for the analysis of these arrays.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>>
>>>> Reading CDF file.
>>>>
>>>> Creating CDF environment
>>>>
>>>> Wait for about 681
>>>>
>>>> Creating package in C:/DATA/mes documents/htagene
>>>>
>>>> Erreur dans copySubstitute(dir(originDir, full.names = TRUE), 
>>>> pkgdir, symbolValues,  :
>>>>
>>>>    'symbolValues' must only contain characters.
>>>>
>>>> Could you please let me know how can fit it?
>>>>
>>>> Thank you in advance!
>>>>
>>>> Best regards,
>>>>
>>>> Trang Tran
>>>>
>>>
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>