[Bioc-devel] new package: huex10stv2cdf

This package was never accepted to Bioconductor for unclear reasons,
but I have had many requests by users to send it to them.  I'm posting
at a public URL for self service.  Here it is, enjoy:

http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz

-Allen

On 5/10/07, Allen Day <allenday at gmail.com> wrote:

I just uploaded this with the web form.

-Allen

Hi Allen,

Allen Day wrote:

This package was never accepted to Bioconductor for unclear reasons,
but I have had many requests by users to send it to them.  I'm posting
at a public URL for self service.  Here it is, enjoy:

http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz

The reason why it was not "accepted" was (after internal discussion
among several Biocore members) that human and mouse exon CDF packages
were already available on the X:MAP site at that time (now it seems
that there is one for Rat too):

      http://xmap.picr.man.ac.uk/cdf

According to their authors, background and control probesets were removed.
It seemed not to be the case with huex10stv2cdf_1.15.0.tar.gz (at least
not at the time it was submitted to BioC):

  > dat <- ReadAffy()
  > cdfName(dat)

  [1] "HuEx-1_0-st-v2"

  > eset <- rma(dat)

  Error in FUN(X[[1411190L]], ...) : subscript out of bounds

However, the authors of the CDF packages available on the X:MAP site didn't
want to publish them in BioC, because (according to them):
  * Affy says CDF for exon arrays are unsupported
  * you either cannot run summarization algorithms or have to remove some
    probesets

Regards,
H.

-Allen

On 5/10/07, Allen Day <allenday at gmail.com> wrote:

I just uploaded this with the web form.

-Allen