Entering edit mode
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
>
