Entering edit mode
This question is better asked on the Bioconductor list
(bioconductor at stat.math.ethz.ch).
James Mcininch wrote:
> I would like to build a package for the HT HG-U133+ PM arrays from
affy,
> but I can't find any good documentation on how to go about it.
Naively
> using makecdfenv's make.cdf.package() causes R to seg-fault.
Without any code or sessionInfo() output, your guess is as good as
mine.
However, I had no problem producing a package.
>
> I'm unfamiliar with the CDF format as such, but I'm guessing that
it's
> changed somewhat because the PM arrays no longer have P/A and
mismatches.
Not AFAIK.
>
> I'm looking to build cdf and probe packages, if possible, but have
yet to
> find any documentation on how to go about this using newer chips.
I've
> also tried building pdInfo packages using pdInfoBuilder from CDF,
csv
> annotation, and tab probe files downloaded from Affy, and
> makePdInfoPackage() fails like so:
>
> makePdInfoPackage(pkg, destDir="/home/mcininch/hthgu133pluspm")
> Creating package in
/home/mcininch/hthgu133pluspm/pd.ht.hg.u133.plus.pm
> Error in data.frame(pmi = batchMat[isPm, "indices"], mmi =
batchMat[!isPm,
> :
> arguments imply differing number of rows: 18230, 180
> Error in is(object, Cl) :
> error in evaluating the argument 'bind.data' in selecting a method
for
> function 'dbSendPreparedQuery'
>
> Any direction to notes or tutorials on the subject?
Other than the help pages for make.cdf.package and makeProbePackage
and
the vignettes? Perhaps there is something unclear in these documents,
in
which case any feedback is appreciated.
Anyway, I'm sending you the packages in a separate email.
Best,
Jim
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
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