[BioC] error with makecdfenv package

[James W. MacDonald]

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
>