[BioC] error with makecdfenv package

[James W. MacDonald]

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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