[BioC] error with makecdfenv package

[cstrato]

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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