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

Thu Feb 21 20:47:09 CET 2013

Lars,

It does not make sense for the cdf environment to have all of those
NA's and it is no wonder the rma code fails.

Now, when I look at the same probeset using affxparser::readCdf, it
does look fine in the sense of pm and mm coordinates (at least at a
casual glance), so I wonder why makecdfenv seems to fail.  Probably
because the custom cdf file is slightly "wrong" - I don't know, and I
don't have to time to track it down.

The solution to this is probably to manually (try to) construct a cdf
environment using the output from affxparser::readCdf (and also
perhaps fix makecdfenv - if there is anything wrong).  This will
require you to play around with some lists and understand the
structure of a cdf environment.  It is not hard, but will require some
studying.  You may decide it is not worth your while - that is up to
you.  It would use the structure of the cdf package returned from
makecdfenv and just fix the cdf environment stored in this package by
constructing it de-novo using affxparser (and not just plug some
holes).

Good luck,
Kasper

On Wed, Feb 20, 2013 at 6:37 AM, Lars Rønn Olsen
<larsronnolsen at gmail.com> wrote:
> 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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