[BioC] Saving Median values to an Affy CEL file

[James MacDonald]

Hi Nathan,

What's your sessionInfo()?

Nathan Haigh wrote:
> James W. MacDonald wrote:
>> Hi Nathan,
>>
>> Nathan Haigh wrote:
>>> I have a need to calculate the median of probes across 4 reps and save
>>> these medians to a single Affy ATH1 CEL file. Can this be done with
>>> bioconductor?
>>>
>> I believe so. See the affxparser package, in particular the
>> createCel() and updateCel() functions.
>>
>> Best,
>>
>> Jim
>>
> 
> Thanks for the head's up.
> 
> I tried installing the package using:
> source("http://bioconductor.org/biocLite.R")
> biocLite(c("affxparser"))
> 
> but get the following error:
> 
> -- snip --
> g++ -I/usr/share/R/include -I/usr/share/R/include -imacros
> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src
> -Ifusion_sdk/calvin_files/data/src
> -Ifusion_sdk/calvin_files/exception/src
> -Ifusion_sdk/calvin_files/fusion/src
> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
> -Ifusion_sdk/calvin_files/parameter/src
> -Ifusion_sdk/calvin_files/parsers/src
> -Ifusion_sdk/calvin_files/portability/src
> -Ifusion_sdk/calvin_files/template/src
> -Ifusion_sdk/calvin_files/utils/src
> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
> -Ifusion_sdk/portability -D_USE_MEM_MAPPING_     -fpic  -g -O2 -O0 -c
> fusion_sdk/calvin_files/data/src/CELData.cpp -o
> fusion_sdk/calvin_files/data/src/CELData.o
> fusion_sdk/calvin_files/data/src/CELData.h:188: error: extra
> qualification 'affymetrix_calvin_io::CelFileData::' on member
> 'GetAlgorithmVersion'
> make: *** [fusion_sdk/calvin_files/data/src/CELData.o] Error 1
> ERROR: compilation failed for package 'affxparser'
> ** Removing '/usr/local/lib/R/site-library/affxparser'
> 
> The downloaded packages are in
>         /tmp/RtmpgblgWq/downloaded_packages
> Warning message:
> installation of package 'affxparser' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> 
> -- end --
> 
> Any ideas if I'm doing something stupid!?
> 
> Thanks
> Nathan
> 
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623