[BioC] Saving Median values to an Affy CEL file

[Nathan Haigh]

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