[BioC] Unable to load in Affymetrix data CEL files with readCelHeader

[Robert Gentleman]

Hi Matt,

Matt K wrote:
> I am having problems reading in some publicly available chromosome X
> titration Nsp chip CEL files. The data are available from the Affymetrix
> website:
> 
> http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx

  I did not see any file there that obviously contained the CEL files, 
can you say what you downloaded (provided the questions below don't 
solve your problem).

> 
> I have not modified the data in anyway. Here is what happens when I try to
> read the data:
> 
>> library(affxparser)
>> path <- "./rawData/3X/Mapping250K_Nsp/"
>> pathnames <- list.files(path=path, pattern="[.](cel|CEL)$",
> full.names=TRUE)
>> pathnames
> [1] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R1.CEL"
> [2] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R2.CEL"
> [3] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R3.CEL"
> [4] "./rawData/3X/Mapping250K_Nsp//NA04626_NSP_R4.CEL"
>> hdr <- readCelHeader(pathnames[1])
> terminate called after throwing an instance of
> 'affymetrix_calvin_exceptions::UnableToOpenFileException'

  That suggests that you may not have read permission on them. Did you 
check and see if you could open those files with any other tool/editor?

   You could just try and open them and read them using standard R tools 
to see if that works (if they are binary CEL files then you will just 
get junk from readLines, but that isn't the issue, you just want to know 
if they can be opened from R).

  Your R is out of date, and this sessionInfo is not correct, as you 
should have had affxparser attached and it is not.  Please don't do 
that, mixing and matching error messages and sessionInfo output makes 
life hard for anyone that wants to help.  Step one is to update R and 
BioC...


> 
> Process R aborted at Tue May 13 15:01:55 2008
> 
> As you see R aborts. The same failure happens when I try to load in any of
> the other CEL files. My R session info is:
> 
>> sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-01-21 r44087)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> Thanks for any help.
> 
> Matt
> 
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org