[BioC] Running time for make.cdf.package

[Kasper Daniel Hansen]

It sounds strange. I would check that it has a traditional PM/MM  
design. I would also check whether there is several groups in each  
unit or only one.

Anyway, since you have tried doing this before, I would suggest using  
for example readCdf from affxparser and then construct the cdf  
environment by hand. That should be somewhat easy, if you have  
experience with cdf environments.

A cdf package is essentially a wrapper around a cdf environment.

Kasper

On Feb 17, 2009, at 9:26 , Jiang, Zhen wrote:

> It's a custom Affy array.  Because of company confidentiality, I'm not
> sure if I should reveal the name.
> The probeset size is only 3.  So the number of probesets are huge
> comparing to normal Affy arrays, which have probeset size about 9 to  
> 11.
> I have made three CDF packages before. The results almost came  
> instantly
> for those three.
> Now this time, it's has been running for more than 3 days and I  
> haven't
> got any output yet.  That's why I'm asking if it is normal or it
> indicates something is wrong with my code or the file.
>
> Thanks,
>
> Zhen Jiang
>
>
> -----Original Message-----
> From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
> Sent: Monday, February 16, 2009 3:24 PM
> To: Jiang, Zhen
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Running time for make.cdf.package
>
> Why don't you tell us the size of the chip, ie. number of probes and
> number of probesets. You might even want to reveal the actual name
> (!). Since it is human, I guess it is pretty big. Your main problem is
> probably memory or a faulty file. In general, making a CDF package is
> pretty quick. I would be shocked if it took more than 1 hour on a
> suitable computer.
>
> Do you get any output, since you are running with verbose = TRUE.
>
> Kasper
>
> On Feb 16, 2009, at 9:57 , Jiang, Zhen wrote:
>
>> Dear list,
>>
>> I have a CDF file of size 404,514KB.  I'm using the following code to
>> build a package from it.
>>
>> library(affy)
>> library(makecdfenv)
>>
>> ## CDF Package
>> make.cdf.package("xxxx.CDF",
>>                species="Homo_sapiens",
>>                version="0.0.1",unlink=TRUE,
>>                verbose=TRUE)
>>
>> It has been running for two and half days.  Is it because the CDF is
>> too
>> large for R to handle or something is wrong with my code?
>> I have successfully build R packages for other much smaller CDF files
>> using the same code, only with different CDF name.
>>
>> The sessionInfo() is listed below.
>>
>>> sessionInfo()
>> R version 2.7.0 (2008-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets
>> methods
>>
>> [8] base
>>
>> other attached packages:
>> [1] makecdfenv_1.18.0    affy_1.18.2          preprocessCore_1.2.1
>> [4] affyio_1.8.1         Biobase_2.0.1
>>
>> Thank you very much.
>>
>> Zhen Jiang
>>
>>
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