[Bioc-devel] new package: huex10stv2cdf

[Allen Day]

ok, thanks for the clarification.  at any rate, i will leave the file
at the url below.

-allen

On 10/31/07, Herve Pages <hpages at fhcrc.org> wrote:
> 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
> >>
> >
> >
>
>


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