[BioC] R crashes when using CDF package generated using makecdfenv

[Lars Rønn Olsen]

Dear Kasper,

Thank you for directing my attention to the missing values in the cdf. Is this cdf completely useless or are there any conceivable situations where this could be a functional cdf? Does it make sense to ignore the NaNs when running affy?

I received this from an author a of paper, for which I am trying to reproduce the results. It is to be applied to the output from ht-hg-u133a chips. Please let me know if more information regarding the set up is useful. No secrets in this regard.

All the best,
Lars

On Feb 19, 2013, at 17:42 , Kasper Daniel Hansen wrote:

> What is your question?
> 
> You do not provide any information about how the cdf file was created.
> Was it an official one from Affymetrix, and just using a custom chip,
> or is it something you or collegeaues have hacked together?  It is
> pretty easy to mess up the cdf specification.
> 
> Anyway, the cdf file reads fine with affxparser (and makecdfenv), but
> if you look at the first entry of the created cdf env from makecdfenv
> you clearly see something is messed up:
> 
>> as.list(testcdf)[[1]]
>          pm  mm
> [1,]  60275 NaN
> [2,] 484839 NaN
> [3,] 423468 NaN
> [4,]  14388 NaN
> [5,]  69256 NaN
> [6,] 134831 NaN
> [7,] 483140 NaN
> [8,] 105347 NaN
> [9,] 315273 NaN
> [10,] 215246 NaN
> [11,] 161557 NaN
> [12,]    NaN NaN
> [13,]    NaN NaN
> [14,]    NaN NaN
> [15,]    NaN NaN
> [16,]    NaN NaN
> [17,]    NaN NaN
> [18,]    NaN NaN
> [19,]    NaN NaN
> [20,]    NaN NaN
> [21,]    NaN NaN
> [22,]    NaN NaN
> 
> I (and probably others as well) are unlikely to try to chase this down
> without some additional information.  I understand if you don't want
> to share details on your custom design / data, but it does make it
> much less likely for someone to help you.
> 
> Kasper
> 
> 
> 
> On Tue, Feb 19, 2013 at 11:23 AM, Lars Rønn Olsen [guest]
> <guest at bioconductor.org> wrote:
>> 
>> Dear Bioconductor/makecdfenv experts,
>> 
>> I am having issues using a cdf package compiled from a custom cdf file using makecdfenv. The code below works fine with other .cdf files, but when I compile a cdf package with the cdf file located here (https://dl.dropbox.com/u/2790735/test.cdf), R simply crashes when I attempt to run rma. Perhaps the cdf file is corrupt?
>> 
>> #Generating cdf package in R
>> library(makecdfenv)
>> make.cdf.package("test.cdf", species = "Homo_sapiens")
>> 
>> #Install in terminal
>> R CMD INSTALL testcdf
>> 
>> #Back in R, attempting to use cdf package
>> library(testcdf)
>> library(affy)
>> matrix <- ReadAffy()
>> matrix at cdfName = "testcdf"
>> matrix.rma <- rma(matrix)
>> #R crashes here (also on other comps)
>> 
>> I'm not sure if/what info from the Mac OSX problem report is relevant, so I uploaded it her (https://dl.dropbox.com/u/2790735/R_error_message.txt).
>> 
>> Any help is greatly appreciated!
>> 
>> Best regards,
>> Lars
>> 
>> -- output of sessionInfo():
>> 
>> R version 2.15.2 (2012-10-26)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] testcdf_1.36.0       AnnotationDbi_1.20.3 affy_1.36.1          Biobase_2.18.0       BiocGenerics_0.4.0   makecdfenv_1.36.0
>> 
>> loaded via a namespace (and not attached):
>> [1] affyio_1.26.0         BiocInstaller_1.8.3   DBI_0.2-5             IRanges_1.16.5        parallel_2.15.2
>> [6] preprocessCore_1.20.0 RSQLite_0.11.2        stats4_2.15.2         tools_2.15.2          zlibbioc_1.4.0
>> 
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
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