[BioC] [R] Need to build package for Affy HT HG-U133+ PM arrays

James W. MacDonald jmacdon at med.umich.edu
Tue Mar 17 18:18:13 CET 2009

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.


> 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.



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James W. MacDonald, M.S.
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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